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BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/abundancebin.manual_bundle.txt

@@ -0,0 +1,236 @@
+# Tool: abundancebin
+software_name: abundancebin
+tier: T1
+domain: t1_backfill_overall
+downloads: 200518
+summary: 
+description: 
+dependencies: libgcc >=13, libstdcxx >=13
+execution_environment: Compiled
+execution_environment_reason: inferred from native/compiled dependencies
+
+## URLs
+home_url: 
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+cli:abundancebin
+## CLI Help Content
+$ conda run -n bioenv_cli abundancebin --help
+[rc=255]
+Usage: ./abundancebin -input (input filename)
+		[-kmer_len (composition len, default 20)]
+		[-output (output file, default inputfile.log)]
+		[-exclude (count)]
+		[-exclude_max (count)]
+		[-OUTPUT_FASTA]
+
+		(if the bin number is known)
+		-bin_num (bin number)
+
+		(or undergo recursive classification)
+		-RECURSIVE_CLASSIFICATION]
+
+
+ERROR conda.cli.main_run:execute(127): `conda run abundancebin --help` failed. (See above for error)
+
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge abundancebin --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+abundancebin 1.0.1 0
+--------------------
+file name   : abundancebin-1.0.1-0.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : 0
+build number: 0
+size        : 20 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-0.tar.bz2
+md5         : e4bae8bd9b44871a240d9d1b27349aef
+dependencies: 
+  - libgcc
+
+
+abundancebin 1.0.1 h2d50403_1
+-----------------------------
+file name   : abundancebin-1.0.1-h2d50403_1.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h2d50403_1
+build number: 1
+size        : 21 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h2d50403_1.tar.bz2
+md5         : 9e79208ca6534e51a3c516c1b8c950e1
+timestamp   : 2018-06-26 05:57:24 UTC
+dependencies: 
+  - libstdcxx-ng >=4.9
+
+
+abundancebin 1.0.1 h4ac6f70_5
+-----------------------------
+file name   : abundancebin-1.0.1-h4ac6f70_5.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h4ac6f70_5
+build number: 5
+size        : 30 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_5.tar.bz2
+md5         : 0aebd6ee78897c669b07a3f13911dfba
+timestamp   : 2023-05-15 01:16:00 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+
+
+abundancebin 1.0.1 h4ac6f70_6
+-----------------------------
+file name   : abundancebin-1.0.1-h4ac6f70_6.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h4ac6f70_6
+build number: 6
+size        : 30 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_6.tar.bz2
+md5         : f174bff04554a6052dad82672eff9ddd
+timestamp   : 2023-05-16 07:10:05 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+
+
+abundancebin 1.0.1 h4ac6f70_7
+-----------------------------
+file name   : abundancebin-1.0.1-h4ac6f70_7.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h4ac6f70_7
+build number: 7
+size        : 30 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h4ac6f70_7.tar.bz2
+md5         : 011e6c8444a5761ab774943fdae04202
+timestamp   : 2024-03-23 01:17:02 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+
+
+abundancebin 1.0.1 h7d875b9_3
+-----------------------------
+file name   : abundancebin-1.0.1-h7d875b9_3.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h7d875b9_3
+build number: 3
+size        : 28 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h7d875b9_3.tar.bz2
+md5         : 905dceb79cd1f982c1e021d33913e004
+timestamp   : 2021-03-27 22:57:26 UTC
+dependencies: 
+  - libgcc-ng >=9.3.0
+  - libstdcxx-ng >=9.3.0
+
+
+abundancebin 1.0.1 h9948957_8
+-----------------------------
+file name   : abundancebin-1.0.1-h9948957_8.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h9948957_8
+build number: 8
+size        : 29 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9948957_8.tar.bz2
+md5         : ed2559099accd2ec3c048889604ddc33
+timestamp   : 2024-12-13 11:23:54 UTC
+dependencies: 
+  - libgcc >=13
+  - libstdcxx >=13
+
+
+abundancebin 1.0.1 h9948957_9
+-----------------------------
+file name   : abundancebin-1.0.1-h9948957_9.conda
+name        : abundancebin
+version     : 1.0.1
+build       : h9948957_9
+build number: 9
+size        : 29 KB
+license     : Copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9948957_9.conda
+md5         : 541d0c0e76c58503e29a685f5e2a5f11
+timestamp   : 2025-08-28 10:03:22 UTC
+dependencies: 
+  - libgcc >=13
+  - libstdcxx >=13
+
+
+abundancebin 1.0.1 h9f5acd7_4
+-----------------------------
+file name   : abundancebin-1.0.1-h9f5acd7_4.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h9f5acd7_4
+build number: 4
+size        : 28 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9f5acd7_4.tar.bz2
+md5         : a414a2ad8c5413bab64496b2a103f8b1
+timestamp   : 2022-02-23 12:49:50 UTC
+dependencies: 
+  - libgcc-ng >=10.3.0
+  - libstdcxx-ng >=10.3.0
+
+
+abundancebin 1.0.1 h9f5acd7_5
+-----------------------------
+file name   : abundancebin-1.0.1-h9f5acd7_5.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : h9f5acd7_5
+build number: 5
+size        : 30 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-h9f5acd7_5.tar.bz2
+md5         : 4068d59b0b4f535ec49010c9c1320b7a
+timestamp   : 2023-05-13 16:22:04 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+
+
+abundancebin 1.0.1 hc9558a2_2
+-----------------------------
+file name   : abundancebin-1.0.1-hc9558a2_2.tar.bz2
+name        : abundancebin
+version     : 1.0.1
+build       : hc9558a2_2
+build number: 2
+size        : 28 KB
+license     : copyright
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/abundancebin-1.0.1-hc9558a2_2.tar.bz2
+md5         : 94a1221c53426a7dc451b4ae18376686
+timestamp   : 2020-08-23 23:13:44 UTC
+dependencies: 
+  - libgcc-ng >=7.5.0
+  - libstdcxx-ng >=7.5.0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anansescanpy.manual_bundle.txt

@@ -0,0 +1,302 @@
+# Tool: anansescanpy
+software_name: anansescanpy
+tier: T1
+domain: single_cell
+downloads: 19494
+summary: implementation of scANANSE for scanpy objects in Python
+description: implementation of scANANSE for scanpy objects in Python
+dependencies: anndata >=0.8.0, numba >=0.56.3, numpy >=1.23.3,<1.24, packaging >=21.3, pandas >=1.4.4, python >=3.8, scanpy >=1.9.1, scipy >=1.9.1
+execution_environment: Python
+execution_environment_reason: inferred from python dependency
+
+## URLs
+home_url: https://github.com/Arts-of-coding/AnanseScanpy
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://github.com/Arts-of-coding/AnanseScanpy
+GitHub - Arts-of-coding/AnanseScanpy: Implementation of scANANSE for Scanpy objects in Python · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} Arts-of-coding / AnanseScanpy Public Notifications You must be signed in to change notification settings Fork 1 Star 7 Code Issues 1 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights Arts-of-coding/AnanseScanpy main Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 103 Commits 103 Commits anansescanpy anansescanpy tests tests vignettes vignettes .codeclimate.yml .codeclimate.yml .gitignore .gitignore LICENSE LICENSE README.md README.md pyproject.toml pyproject.toml requirements.yaml requirements.yaml View all files Repository files navigation README Apache-2.0 license AnanseScanpy package: implementation of scANANSE for Scanpy objects in Python Installation The most straightforward way to install the most recent version of AnanseScanpy is via conda using PyPI. Install package through Conda If you have not used Bioconda before, first set up the necessary channels (in this order!). You only have to do this once. $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge Then install AnanseScanpy with: $ conda install anansescanpy Install package through PyPI $ pip install anansescanpy Install package through GitHub $ git clone https://github.com/Arts-of-coding/AnanseScanpy.git $ cd AnanseScanpy $ conda env create -f requirements.yaml $ conda activate AnanseScanpy $ pip install -e . Install Jupyter Notebook $ pip install jupyter Start using the package Run the package either in the console $ python3 Or run the package in jupyter notebook $ jupyter notebook For extended documentation see our ipynb vignette with PBMC sample data Of which the sample data can be downloaded $ wget https://zenodo.org/records/7575107/files/rna_PBMC.h5ad?download=1 -O scANANSE/rna_PBMC.h5ad $ wget https://zenodo.org/records/7575107/files/atac_PBMC.h5ad?download=1 -O scANANSE/atac_PBMC.h5ad installing and running anansnake Follow the instructions its respective github page, https://github.com/vanheeringen-lab/anansnake Next automatically use the generated files to run GRN analysis using your single cell cluster data: snakemake --use-conda --conda-frontend mamba \ --configfile scANANSE/analysis/config.yaml \ --snakefile scANANSE/anansnake/Snakefile \ --resources mem_mb=48_000 --cores 12 Thanks to: Jos Smits and his Seurat equivalent of this package https://github.com/JGASmits/AnanseSeurat Siebren Frohlich and his anansnake implementation https://github.com/vanheeringen-lab/anansnake How to cite this software: Smits JGA, Arts JA, Frölich S et al. scANANSE gene regulatory network and motif analysis of single-cell clusters [version 1; peer review: awaiting peer review]. F1000Research 2023, 12:243 ( https://doi.org/10.12688/f1000research.130530.1 ) About Implementation of scANANSE for Scanpy objects in Python Resources Readme License Apache-2.0 license Uh oh! There was an error while loading. Please reload this page . Activity Stars 7 stars Watchers 1 watching Forks 1 fork Report repository Releases 1 Release v1.0.0 Latest Jan 12, 2023 Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Jupyter Notebook 98.6% Python 1.4% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge anansescanpy --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+anansescanpy 0.1.2 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.1.2-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.1.2
+build       : pyhdfd78af_0
+build number: 0
+size        : 17 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.2-pyhdfd78af_0.tar.bz2
+md5         : 94e544c469ed8e38d93af86e39142640
+timestamp   : 2022-11-02 13:31:51 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.1.4 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.1.4-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.1.4
+build       : pyhdfd78af_0
+build number: 0
+size        : 18 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.4-pyhdfd78af_0.tar.bz2
+md5         : dabf998a4b44aaf574bf27f6b4dac898
+timestamp   : 2022-11-08 16:28:41 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.1.5 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.1.5-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.1.5
+build       : pyhdfd78af_0
+build number: 0
+size        : 18 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.5-pyhdfd78af_0.tar.bz2
+md5         : 9ca60664683afd691fa37b8446442d8d
+timestamp   : 2022-11-10 18:24:24 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.1.8 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.1.8-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.1.8
+build       : pyhdfd78af_0
+build number: 0
+size        : 18 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.8-pyhdfd78af_0.tar.bz2
+md5         : c67bedc2a1ae2b67780417fb991dc16f
+timestamp   : 2022-11-17 10:20:45 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.1.9 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.1.9-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.1.9
+build       : pyhdfd78af_0
+build number: 0
+size        : 22 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.1.9-pyhdfd78af_0.tar.bz2
+md5         : d0230b9e959ad14d5d8bed38707477af
+timestamp   : 2022-11-30 11:35:23 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.2.0 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.2.0-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.2.0
+build       : pyhdfd78af_0
+build number: 0
+size        : 22 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.0-pyhdfd78af_0.tar.bz2
+md5         : 6b0b8c429beefcb68c41ff4eb6fecd49
+timestamp   : 2022-11-30 16:29:05 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.2.1 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.2.1-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.2.1
+build       : pyhdfd78af_0
+build number: 0
+size        : 22 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.1-pyhdfd78af_0.tar.bz2
+md5         : ec1243eb42080bd2cf726fea4904b750
+timestamp   : 2022-12-06 10:42:18 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.2.2 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.2.2-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.2.2
+build       : pyhdfd78af_0
+build number: 0
+size        : 22 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.2-pyhdfd78af_0.tar.bz2
+md5         : c9e6a6a58ac357ed8e47ceb456446376
+timestamp   : 2022-12-08 11:30:36 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.2.3 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.2.3-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.2.3
+build       : pyhdfd78af_0
+build number: 0
+size        : 23 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.3-pyhdfd78af_0.tar.bz2
+md5         : 17d0cf700432ee627b971670aa634101
+timestamp   : 2022-12-16 20:23:20 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - jupyterlab >=3.3.4
+  - numpy >=1.23.3
+  - pandas >=1.4.4
+  - python >=3.6
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 0.2.6 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-0.2.6-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 0.2.6
+build       : pyhdfd78af_0
+build number: 0
+size        : 23 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-0.2.6-pyhdfd78af_0.tar.bz2
+md5         : f1bf5bb9e707f0e156126871d399fde5
+timestamp   : 2023-01-12 10:08:13 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - numba >=0.56.3
+  - numpy >=1.23.3,<1.24
+  - packaging >=21.3
+  - pandas >=1.4.4
+  - python >=3.8
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 1.0.0 pyhdfd78af_0
+-------------------------------
+file name   : anansescanpy-1.0.0-pyhdfd78af_0.tar.bz2
+name        : anansescanpy
+version     : 1.0.0
+build       : pyhdfd78af_0
+build number: 0
+size        : 23 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-1.0.0-pyhdfd78af_0.tar.bz2
+md5         : 5ad86690b5f633eba40037872b3dbc9a
+timestamp   : 2023-01-12 11:35:52 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - numba >=0.56.3
+  - numpy >=1.23.3,<1.24
+  - packaging >=21.3
+  - pandas >=1.4.4
+  - python >=3.8
+  - scanpy >=1.9.1
+  - scipy >=1.9.1
+
+
+anansescanpy 1.0.0 pyhdfd78af_1
+-------------------------------
+file name   : anansescanpy-1.0.0-pyhdfd78af_1.tar.bz2
+name        : anansescanpy
+version     : 1.0.0
+build       : pyhdfd78af_1
+build number: 1
+size        : 23 KB
+license     : Apache-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anansescanpy-1.0.0-pyhdfd78af_1.tar.bz2
+md5         : cc310593d651e949381a29f775ff785c
+timestamp   : 2024-04-03 05:46:48 UTC
+dependencies: 
+  - anndata >=0.8.0
+  - numba >=0.56.3
+  - numpy >=1.23.3,<1.24
+  - packaging >=21.3
+  - pandas >=1.4.4
+  - python >=3.8
+  - scanpy >=1.9.1
+  - scipy >=1.9.1

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/anarci.manual_bundle.txt

@@ -0,0 +1,140 @@
+# Tool: anarci
+software_name: anarci
+tier: T1
+domain: t1_backfill_overall
+downloads: 262463
+summary: ANARCI: Antibody Numbering and Antigen Receptor ClassIfication
+description: ANARCI: Antibody Numbering and Antigen Receptor ClassIfication
+dependencies: biopython, hmmer >=3.3.2, python
+execution_environment: Python
+execution_environment_reason: inferred from python dependency
+
+## URLs
+home_url: http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/
+SAbPred: ANARCI --> --> Web Apps ABodyBuilder-ML ABodyBuilder2 TCRBuilder2 NanoBodyBuilder2 PEARS ANARCI ANARCII-LM SCALOP TAP Hu-mAb Humatch p-IgGen Databases SAbDab Thera-SAbDab CoV-AbDab OAS Database OTS Database STCRDab PLAbDab PLAbDab-nano GitHub ImmuneBuilder ABlooper AbLang Paragraph DLAB More OPIG Repos ... Downloads Job Queue About ^ ANARCI (Legacy version) >    About ANARCI A ntigen receptor N umbering A nd R eceptor C lassificat I on. ANARCI is a tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains. Use the form below to identify domains and annotate them with either the IMGT, Chothia, Kabat, Martin (Enhanced Chothia) or AHo numbering scheme. TCR sequences can only be numbered with IMGT or AHo schemes. ANARCI aligns a given sequence to a database of Hidden Markov Models that describe the germline sequences of antibody and TCR domain types. The most significant alignment predicts the domain type and species (*) of the input sequence. The ANARCI Python package is freely available on Github . For a full description of the pipeline, or if you use this software, please refer to: Dunbar J and Deane CM. ANARCI: Antigen receptor numbering and receptor classification. Bioinformatics (2016) >    Sequence submission form The ANARCI web application restricts germline species to human and mouse to ensure numbering remains consistent over time. If you wish to use other species' germlines you can do this using the ANARCI Python package available on GitHub Submit single sequence: load example or upload multiple sequences as a fasta file: ' followed by the amino acid sequence (on multiple lines if required)."> Choose a numbering scheme: IMGT Kabat Chothia Martin AHo Choose an output format: Comma separated value (csv) file (horizontal format) Plain text (txt) file (vertical format) Restrict to immunoglobulin domains only Annotate SAbPred paper: Dunbar, J. et al (2016). Nucleic Acids Res. 44. W474-W478 [link] We use cookies to collect usage statistics for this website. By continuing to browse this site you agree to our use of cookies. For more details about cookies see our privacy policy . Continue
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge anarci --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+anarci 2020.04.23 py_0
+----------------------
+file name   : anarci-2020.04.23-py_0.tar.bz2
+name        : anarci
+version     : 2020.04.23
+build       : py_0
+build number: 0
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_0.tar.bz2
+md5         : d72fec6243f13682e13a08f1f43459d9
+timestamp   : 2020-06-12 12:32:14 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.1
+  - python
+
+
+anarci 2020.04.23 py_1
+----------------------
+file name   : anarci-2020.04.23-py_1.tar.bz2
+name        : anarci
+version     : 2020.04.23
+build       : py_1
+build number: 1
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_1.tar.bz2
+md5         : fdc084269eb3669d2c667c7a8b725ee5
+timestamp   : 2020-07-03 09:09:46 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.1
+  - python
+
+
+anarci 2020.04.23 py_2
+----------------------
+file name   : anarci-2020.04.23-py_2.tar.bz2
+name        : anarci
+version     : 2020.04.23
+build       : py_2
+build number: 2
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_2.tar.bz2
+md5         : 289d79dcfe14d8eb1b8c525d49080048
+timestamp   : 2020-07-09 22:17:48 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.1
+  - python
+
+
+anarci 2020.04.23 py_3
+----------------------
+file name   : anarci-2020.04.23-py_3.tar.bz2
+name        : anarci
+version     : 2020.04.23
+build       : py_3
+build number: 3
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2020.04.23-py_3.tar.bz2
+md5         : 75d82b9436922718d47f5b1bb6b75d24
+timestamp   : 2020-07-26 04:30:32 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.1
+  - python
+
+
+anarci 2021.02.04 pyhdfd78af_0
+------------------------------
+file name   : anarci-2021.02.04-pyhdfd78af_0.tar.bz2
+name        : anarci
+version     : 2021.02.04
+build       : pyhdfd78af_0
+build number: 0
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2021.02.04-pyhdfd78af_0.tar.bz2
+md5         : 34b8c4648667bff833a01104632273f1
+timestamp   : 2021-07-20 09:18:06 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.1
+  - python
+
+
+anarci 2024.05.21 pyhdfd78af_0
+------------------------------
+file name   : anarci-2024.05.21-pyhdfd78af_0.tar.bz2
+name        : anarci
+version     : 2024.05.21
+build       : pyhdfd78af_0
+build number: 0
+size        : 1.1 MB
+license     : BSD-3-Clause
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/anarci-2024.05.21-pyhdfd78af_0.tar.bz2
+md5         : 3342c9d8e5917b8c080891b5c574f4eb
+timestamp   : 2024-12-06 19:15:23 UTC
+dependencies: 
+  - biopython
+  - hmmer >=3.3.2
+  - python

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bactopia.manual_bundle.txt

@@ -0,0 +1,634 @@
+# Tool: bactopia
+software_name: bactopia
+tier: T1
+domain: t1_backfill_overall
+downloads: 235804
+summary: Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
+description: Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
+dependencies: bactopia-py 1.5.0.*, conda >=22.11.0, coreutils, mamba >=1.1.0, nextflow >=23,<24, python >=3.9,<3.13, sed, wget
+execution_environment: Python
+execution_environment_reason: inferred from python dependency
+
+## URLs
+home_url: https://github.com/bactopia/bactopia
+doc_url: 
+dev_url: https://github.com/bactopia/bactopia/
+
+## URL Docs Extract
+### https://github.com/bactopia/bactopia
+GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bactopia / bactopia Public Notifications You must be signed in to change notification settings Fork 80 Star 505 Code Issues 104 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bactopia/bactopia master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,633 Commits 1,633 Commits .claude .claude .github .github .vscode .vscode bin bin conf conf data data modules modules subworkflows subworkflows tests tests workflows workflows .gitignore .gitignore CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CLAUDE.md CLAUDE.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md catalog.json catalog.json environment.yml environment.yml llms.txt llms.txt main.nf main.nf nextflow.config nextflow.config nextflow_schema.json nextflow_schema.json View all files Repository files navigation README Code of conduct Contributing MIT license Bactopia Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main parts: Bactopia Analysis Pipeline , and Bactopia Tools . Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow , input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more. Bactopia Tools are a set a independent workflows for comparative analyses. The comparative analyses may include summary reports, pan-genome, or phylogenetic tree construction. Using the predictable output structure of Bactopia you can pick and choose which samples to include for processing with a Bactopia Tool. Bactopia was inspired by Staphopia , a workflow we (Tim Read and myself) released that targets Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start. Documentation Documentation for Bactopia is available at https://bactopia.io/ . The documentation includes a tutorial replicating Staphopia and a complete overview of Bactopia. I highly encourage you check it out! Quick Start mamba create -y -n bactopia -c conda-forge -c bioconda bactopia conda activate bactopia bactopia datasets # Paired-end bactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \ --datasets datasets/ --outdir OUTDIR # Single-End bactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR # Multiple Samples bactopia prepare MY-FASTQS/ &gt; fastqs.txt bactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR # Single ENA/SRA Experiment bactopia --accession SRX000000 --datasets datasets --outdir OUTDIR # Multiple ENA/SRA Experiments bactopia search "staphylococcus aureus" &gt; accessions.txt bactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR} Installation Bactopia has a lot of tools built into its workflow. As you can imagine, all these tools lead to numerous dependencies, and navigating dependencies can often turn into a very frustrating process. With this in mind, from the onset Bactopia was developed to only include programs that are installable using Conda . Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. In other words, it makes it super easy to get the tools you need installed! The official Conda documentation is a good starting point for getting started with Conda. Bactopia has been tested using the Miniforge installer , but the Anaconda installer should work the same. Once you have Conda all set up, you are ready to create an environment for Bactopia. # Recommended mamba create -n bactopia -c conda-forge -c bioconda bactopia # or with standard conda conda create -n bactopia -c conda-forge -c bioconda bactopia After a few minutes you will have a new conda environment suitably named bactopia . To activate this environment, you will can use the following command: conda activate bactopia And voilà, you are all set to get started processing your data! Please Cite Datasets and Tools If you have used Bactopia in your work, please be sure to cite any datasets or tools you may have used. A list of each dataset/tool used by Bactopia has been made available . If a citation needs to be updated please let me know! Acknowledgements Bactopia is truly a case of "standing upon the shoulders of giants" . Nearly every component of Bactopia was created by others and made freely available to the public. I would like to personally extend my many thanks and gratitude to the authors of these software packages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!) if we ever encounter one another in person. Really, thank you very much! Alternatives In case Bactopia doesn't fit your needs, here are some alternatives you can checkout. I personally haven't used them, but you might find them to fit your needs! If you ran into issues using Bactopia, please feel free to reach out ! AQUAMIS Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS. Genes . 2021;12. doi:10.3390/genes12050644 ASA³P Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 2020;16:e1007134. https://doi.org/10.1371/journal.pcbi.1007134 . MicroPIPE Murigneux V, Roberts LW, Forde BM, Phan M-D, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics , 22(1), 474. (2021) https://doi.org/10.1186/s12864-021-07767-z Nullarbor Seemann T, Goncalves da Silva A, Bulach DM, Schultz MB, Kwong JC, Howden BP. Nullarbor Github https://github.com/tseemann/nullarbor ProkEvo Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ , e11376 (2021) https://doi.org/10.7717/peerj.11376 Public Health Bacterial Genomics Libuit K, Ambrosio F, Kapsak C Public Health Bacterial Genomics GitHub https://github.com/theiagen/public_health_bacterial_genomics rMAP Sserwadda I, Mboowa G rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial Genomics , 7(6). (2021) https://doi.org/10.1099/mgen.0.000583 TORMES Quijada NM, Rodríguez-L��zaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics 2019;35:4207–12. https://doi.org/10.1093/bioinformatics/btz220 . Feedback Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the Issue Tracker . License MIT License Citation Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems . 5 (2020), https://doi.org/10.1128/mSystems.00190-20 . Author Robert A. Petit III BlueSky: @rpetit3 Funding Support for this project came (in part) from an Emory Public Health Bioinformatics Fellowship funded by the CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacity , the Wyoming Public Health Division , the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE) , and the CZI Open Science Program (EOSS6) . About A flexible pipeline for complete analysis of bacterial genomes bactopia.io Topics nextflow conda bioconda bacterial-genomes fastqs Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 505 stars Watchers 14 watching Forks 80 forks Report repository Releases 52 v4.0.0 Latest Apr 29, 2026 + 51 releases Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Nextflow 92.9% Perl 4.8% Shell 2.0% Python 0.3% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+### https://github.com/bactopia/bactopia/
+GitHub - bactopia/bactopia: A flexible pipeline for complete analysis of bacterial genomes · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bactopia / bactopia Public Notifications You must be signed in to change notification settings Fork 80 Star 505 Code Issues 104 Pull requests 0 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bactopia/bactopia master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 1,633 Commits 1,633 Commits .claude .claude .github .github .vscode .vscode bin bin conf conf data data modules modules subworkflows subworkflows tests tests workflows workflows .gitignore .gitignore CHANGELOG.md CHANGELOG.md CITATION.cff CITATION.cff CLAUDE.md CLAUDE.md CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md CONTRIBUTING.md CONTRIBUTING.md LICENSE LICENSE README.md README.md catalog.json catalog.json environment.yml environment.yml llms.txt llms.txt main.nf main.nf nextflow.config nextflow.config nextflow_schema.json nextflow_schema.json View all files Repository files navigation README Code of conduct Contributing MIT license Bactopia Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main parts: Bactopia Analysis Pipeline , and Bactopia Tools . Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow , input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more. Bactopia Tools are a set a independent workflows for comparative analyses. The comparative analyses may include summary reports, pan-genome, or phylogenetic tree construction. Using the predictable output structure of Bactopia you can pick and choose which samples to include for processing with a Bactopia Tool. Bactopia was inspired by Staphopia , a workflow we (Tim Read and myself) released that targets Staphylococcus aureus genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start. Documentation Documentation for Bactopia is available at https://bactopia.io/ . The documentation includes a tutorial replicating Staphopia and a complete overview of Bactopia. I highly encourage you check it out! Quick Start mamba create -y -n bactopia -c conda-forge -c bioconda bactopia conda activate bactopia bactopia datasets # Paired-end bactopia --R1 R1.fastq.gz --R2 R2.fastq.gz --sample SAMPLE_NAME \ --datasets datasets/ --outdir OUTDIR # Single-End bactopia --SE SAMPLE.fastq.gz --sample SAMPLE --datasets datasets/ --outdir OUTDIR # Multiple Samples bactopia prepare MY-FASTQS/ &gt; fastqs.txt bactopia --fastqs fastqs.txt --datasets datasets --outdir OUTDIR # Single ENA/SRA Experiment bactopia --accession SRX000000 --datasets datasets --outdir OUTDIR # Multiple ENA/SRA Experiments bactopia search "staphylococcus aureus" &gt; accessions.txt bactopia --accessions accessions.txt --dataset datasets --outdir ${OUTDIR} Installation Bactopia has a lot of tools built into its workflow. As you can imagine, all these tools lead to numerous dependencies, and navigating dependencies can often turn into a very frustrating process. With this in mind, from the onset Bactopia was developed to only include programs that are installable using Conda . Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. In other words, it makes it super easy to get the tools you need installed! The official Conda documentation is a good starting point for getting started with Conda. Bactopia has been tested using the Miniforge installer , but the Anaconda installer should work the same. Once you have Conda all set up, you are ready to create an environment for Bactopia. # Recommended mamba create -n bactopia -c conda-forge -c bioconda bactopia # or with standard conda conda create -n bactopia -c conda-forge -c bioconda bactopia After a few minutes you will have a new conda environment suitably named bactopia . To activate this environment, you will can use the following command: conda activate bactopia And voilà, you are all set to get started processing your data! Please Cite Datasets and Tools If you have used Bactopia in your work, please be sure to cite any datasets or tools you may have used. A list of each dataset/tool used by Bactopia has been made available . If a citation needs to be updated please let me know! Acknowledgements Bactopia is truly a case of "standing upon the shoulders of giants" . Nearly every component of Bactopia was created by others and made freely available to the public. I would like to personally extend my many thanks and gratitude to the authors of these software packages and public datasets. If you've made it this far, I owe you a beer 🍻 (or coffee ☕!) if we ever encounter one another in person. Really, thank you very much! Alternatives In case Bactopia doesn't fit your needs, here are some alternatives you can checkout. I personally haven't used them, but you might find them to fit your needs! If you ran into issues using Bactopia, please feel free to reach out ! AQUAMIS Deneke C, Brendebach H, Uelze L, Borowiak M, Malorny B, Tausch SH. Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS. Genes . 2021;12. doi:10.3390/genes12050644 ASA³P Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A. ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Comput Biol 2020;16:e1007134. https://doi.org/10.1371/journal.pcbi.1007134 . MicroPIPE Murigneux V, Roberts LW, Forde BM, Phan M-D, Nhu NTK, Irwin AD, Harris PNA, Paterson DL, Schembri MA, Whiley DM, Beatson SA MicroPIPE: validating an end-to-end workflow for high-quality complete bacterial genome construction. BMC Genomics , 22(1), 474. (2021) https://doi.org/10.1186/s12864-021-07767-z Nullarbor Seemann T, Goncalves da Silva A, Bulach DM, Schultz MB, Kwong JC, Howden BP. Nullarbor Github https://github.com/tseemann/nullarbor ProkEvo Pavlovikj N, Gomes-Neto JC, Deogun JS, Benson AK ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses. PeerJ , e11376 (2021) https://doi.org/10.7717/peerj.11376 Public Health Bacterial Genomics Libuit K, Ambrosio F, Kapsak C Public Health Bacterial Genomics GitHub https://github.com/theiagen/public_health_bacterial_genomics rMAP Sserwadda I, Mboowa G rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial Genomics , 7(6). (2021) https://doi.org/10.1099/mgen.0.000583 TORMES Quijada NM, Rodríguez-Lázaro D, Eiros JM, Hernández M. TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics 2019;35:4207–12. https://doi.org/10.1093/bioinformatics/btz220 . Feedback Your feedback is very valuable! If you run into any issues using Bactopia, have questions, or have some ideas to improve Bactopia, I highly encourage you to submit it to the Issue Tracker . License MIT License Citation Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems . 5 (2020), https://doi.org/10.1128/mSystems.00190-20 . Author Robert A. Petit III BlueSky: @rpetit3 Funding Support for this project came (in part) from an Emory Public Health Bioinformatics Fellowship funded by the CDC Emerging Infections Program (U50CK000485) PPHF/ACA: Enhancing Epidemiology and Laboratory Capacity , the Wyoming Public Health Division , the Center for Applied Pathogen Epidemiology and Outbreak Control (CAPE) , and the CZI Open Science Program (EOSS6) . About A flexible pipeline for complete analysis of bacterial genomes bactopia.io Topics nextflow conda bioconda bacterial-genomes fastqs Resources Readme License MIT license Code of conduct Code of conduct Contributing Contributing Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 505 stars Watchers 14 watching Forks 80 forks Report repository Releases 52 v4.0.0 Latest Apr 29, 2026 + 51 releases Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Nextflow 92.9% Perl 4.8% Shell 2.0% Python 0.3% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bactopia --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bactopia 1.0.1 0
+----------------
+file name   : bactopia-1.0.1-0.tar.bz2
+name        : bactopia
+version     : 1.0.1
+build       : 0
+build number: 0
+size        : 16 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.0.1-0.tar.bz2
+md5         : c71a2086a9da252582e8a7b249c35a36
+timestamp   : 2019-09-12 17:12:41 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - python >3.6
+  - unzip
+  - urllib3
+  - wget
+
+
+bactopia 1.1.0 0
+----------------
+file name   : bactopia-1.1.0-0.tar.bz2
+name        : bactopia
+version     : 1.1.0
+build       : 0
+build number: 0
+size        : 16 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.1.0-0.tar.bz2
+md5         : 369a66a11ce796a9969193acf910f16a
+timestamp   : 2019-09-19 17:50:40 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - python >3.6
+  - unzip
+  - urllib3
+  - wget
+
+
+bactopia 1.1.0 1
+----------------
+file name   : bactopia-1.1.0-1.tar.bz2
+name        : bactopia
+version     : 1.1.0
+build       : 1
+build number: 1
+size        : 16 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.1.0-1.tar.bz2
+md5         : 7e9733c18e49a22e6af948bcb15d7f52
+timestamp   : 2019-09-20 10:33:48 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - unzip
+  - urllib3
+  - wget
+
+
+bactopia 1.2.0 0
+----------------
+file name   : bactopia-1.2.0-0.tar.bz2
+name        : bactopia
+version     : 1.2.0
+build       : 0
+build number: 0
+size        : 18 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.0-0.tar.bz2
+md5         : 27f23d4cf00e468e168781ec0a175245
+timestamp   : 2019-10-17 06:35:24 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.2.1 0
+----------------
+file name   : bactopia-1.2.1-0.tar.bz2
+name        : bactopia
+version     : 1.2.1
+build       : 0
+build number: 0
+size        : 19 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.1-0.tar.bz2
+md5         : 4229ff77d6472b0eaa1401fe6cbd181d
+timestamp   : 2019-10-17 18:25:56 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.2.2 0
+----------------
+file name   : bactopia-1.2.2-0.tar.bz2
+name        : bactopia
+version     : 1.2.2
+build       : 0
+build number: 0
+size        : 19 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.2-0.tar.bz2
+md5         : 6a0831fd73b90731e7861adbc0a317fd
+timestamp   : 2019-10-24 16:41:14 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.2.4 0
+----------------
+file name   : bactopia-1.2.4-0.tar.bz2
+name        : bactopia
+version     : 1.2.4
+build       : 0
+build number: 0
+size        : 19 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.2.4-0.tar.bz2
+md5         : 785af4c19c070e416a2c8ba1937bdd4e
+timestamp   : 2019-12-25 12:11:54 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.3.0 0
+----------------
+file name   : bactopia-1.3.0-0.tar.bz2
+name        : bactopia
+version     : 1.3.0
+build       : 0
+build number: 0
+size        : 976 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.3.0-0.tar.bz2
+md5         : fbf60bbc5eb5503329511d55641da78d
+timestamp   : 2020-02-19 19:11:26 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.3.1 0
+----------------
+file name   : bactopia-1.3.1-0.tar.bz2
+name        : bactopia
+version     : 1.3.1
+build       : 0
+build number: 0
+size        : 1.3 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.3.1-0.tar.bz2
+md5         : 058aac793476515d9d8ac8d0f12ee555
+timestamp   : 2020-04-21 02:01:30 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.0 0
+----------------
+file name   : bactopia-1.4.0-0.tar.bz2
+name        : bactopia
+version     : 1.4.0
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.0-0.tar.bz2
+md5         : ac19f7bc58c0a2210a9937c3908611c6
+timestamp   : 2020-07-02 03:56:08 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.1 0
+----------------
+file name   : bactopia-1.4.1-0.tar.bz2
+name        : bactopia
+version     : 1.4.1
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.1-0.tar.bz2
+md5         : 74d9752829d8cad228d434a0b0ac974c
+timestamp   : 2020-08-06 22:12:14 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.2 0
+----------------
+file name   : bactopia-1.4.2-0.tar.bz2
+name        : bactopia
+version     : 1.4.2
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.2-0.tar.bz2
+md5         : a243ceb1c06106788730e7650ff2da31
+timestamp   : 2020-08-10 15:21:39 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.3 0
+----------------
+file name   : bactopia-1.4.3-0.tar.bz2
+name        : bactopia
+version     : 1.4.3
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.3-0.tar.bz2
+md5         : 1d58e12b4516f08e71fdfe5e9fc4c028
+timestamp   : 2020-08-13 16:13:27 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.4 0
+----------------
+file name   : bactopia-1.4.4-0.tar.bz2
+name        : bactopia
+version     : 1.4.4
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.4-0.tar.bz2
+md5         : 1abf674e73de4764a000e51fd680477e
+timestamp   : 2020-08-13 21:13:09 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.5 0
+----------------
+file name   : bactopia-1.4.5-0.tar.bz2
+name        : bactopia
+version     : 1.4.5
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.5-0.tar.bz2
+md5         : 78281c39fcea4d3ce374189573276d96
+timestamp   : 2020-08-13 22:16:30 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.6 0
+----------------
+file name   : bactopia-1.4.6-0.tar.bz2
+name        : bactopia
+version     : 1.4.6
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.6-0.tar.bz2
+md5         : ddebe60bd426ec89c4a7c78ae3580176
+timestamp   : 2020-08-17 21:13:33 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.7 0
+----------------
+file name   : bactopia-1.4.7-0.tar.bz2
+name        : bactopia
+version     : 1.4.7
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.7-0.tar.bz2
+md5         : 1b1f2c886d3f7e79bd0249a74af887fb
+timestamp   : 2020-08-18 00:24:01 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.8 0
+----------------
+file name   : bactopia-1.4.8-0.tar.bz2
+name        : bactopia
+version     : 1.4.8
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.8-0.tar.bz2
+md5         : 4373b9fb058f4fdf1eedf007785995e8
+timestamp   : 2020-08-21 02:17:30 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lxml
+  - mash
+  - ncbi-genome-download
+  - nextflow
+  - pysam >=0.15.3
+  - python >3.6
+  - requests
+  - unzip
+  - wget
+
+
+bactopia 1.4.9 0
+----------------
+file name   : bactopia-1.4.9-0.tar.bz2
+name        : bactopia
+version     : 1.4.9
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bactopia-1.4.9-0.tar.bz2
+md5         : fa1ca25a5d109c0764c4699709698dae
+timestamp   : 2020-08-23 15:15:53 UTC
+dependencies: 
+  - ariba
+  - beautifulsoup4
+  - biopython
+  - blast
+  - bowtie2 <2.4.0
+  - cd-hit
+  - conda
+  - executor
+  - lx

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bcbio-nextgen.manual_bundle.txt

@@ -0,0 +1,731 @@
+# Tool: bcbio-nextgen
+software_name: bcbio-nextgen
+tier: T1
+domain: t1_backfill_overall
+downloads: 415872
+summary: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
+description: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
+dependencies: arrow, beautifulsoup4, bioblend, biopython, boto, cyvcf2, dnapi, fadapa, geneimpacts, gffutils, h5py, htslib, ipyparallel 6.3.0.*, ipython-cluster-helper 0.6.4 py_0, joblib >=0.12, logbook, matplotlib-base, mock, msgpack-python, openssl <3.0.0, pandas, pip, psutil, py, pybedtools, pycrypto, pysam >=0.13.0, pytest, pytest-cov >=2.6.1, pytest-mock, python, python-dateutil >=2.5.0, pyvcf, pyyaml, requests, scipy >=1.3.0, seaborn, seqcluster, statsmodels, tabulate, toolz, yamllint
+execution_environment: Python
+execution_environment_reason: inferred from python dependency
+
+## URLs
+home_url: https://github.com/bcbio/bcbio-nextgen
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://github.com/bcbio/bcbio-nextgen
+GitHub - bcbio/bcbio-nextgen: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} bcbio / bcbio-nextgen Public Notifications You must be signed in to change notification settings Fork 355 Star 1k Code Issues 129 Pull requests 4 Actions Projects Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights bcbio/bcbio-nextgen master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 8,579 Commits 8,579 Commits .github .github artwork artwork bcbio bcbio config config docs docs scripts scripts tests tests .gitignore .gitignore .readthedocs.yml .readthedocs.yml .travis.yml .travis.yml CODE_OF_CONDUCT.md CODE_OF_CONDUCT.md HISTORY.md HISTORY.md LICENSE.txt LICENSE.txt MANIFEST.in MANIFEST.in README.md README.md Vagrantfile Vagrantfile requirements-conda.txt requirements-conda.txt requirements-dev.txt requirements-dev.txt requirements.txt requirements.txt setup.cfg setup.cfg setup.py setup.py View all files Repository files navigation README Code of conduct MIT license Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. NOTE!!!! Please read the notice of discontinuation of this project - 08-16-2024 Features Community developed: We welcome contributors with the goal of overcoming the biological, algorithmic and computational challenges that face individual developers working on complex pipelines in quickly changing research areas. See our users page for examples of bcbio-nextgen deployments, and the developer documentation for tips on contributing. Installation: A single installer script prepares all third party software, data libraries and system configuration files. Automated validation : Compare variant calls against common reference materials or sample specific SNP arrays to ensure call correctness. Incorporation of multiple approaches for alignment, preparation and variant calling enable unbiased comparisons of algorithms. Distributed: Focus on parallel analysis and scaling to handle large population studies and whole genome analysis. Runs on single multicore computers, in compute clusters using IPython parallel , or on the Amazon cloud. See the parallel documentation for full details. Multiple analysis algorithms: bcbio-nextgen provides configurable variant calling (small and copy number), RNA-seq, ATAC-seq, , BS-Seq, SC RNA-seq, and small RNA pipelines . Quick start Install bcbio-nextgen with all tool dependencies and data files: wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \ --genomes hg38 --aligners bwa --aligners bowtie2 producing an editable system configuration file referencing the installed software, data and system information. Automatically create a processing description of sample FASTQ and BAM files from your project, and a CSV file of sample metadata: bcbio_nextgen.py -w template freebayes-variant project1.csv sample1.bam sample2_1.fq sample2_2.fq This produces a sample description file containing pipeline configuration options . Run analysis, distributed across 8 local cores: cd project1/work bcbio_nextgen.py ../config/project1.yaml -n 8 Documentation See the full documentation and longer analysis-based articles . We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list . Contributors Miika Ahdesmaki , AstraZeneca Luca Beltrame , IRCCS "Mario Negri" Institute for Pharmacological Research, Milan, Italy Christian Brueffer , Lund University, Lund, Sweden Alla Bushoy , AstraZeneca Guillermo Carrasco , Science for Life Laboratory, Stockholm Nick Carriero , Simons Foundation Brad Chapman , Harvard Chan Bioinformatics Core Saket Choudhary , University Of Southern California Peter Cock , The James Hutton Institute Matthias De Smet , Center for Medical Genetics, Ghent University Hospital, Belgium Matt Edwards , MIT Mario Giovacchini , Science for Life Laboratory, Stockholm Karl Gutwin , Biogen Jeff Hammerbacher , Icahn School of Medicine at Mount Sinai Oliver Hofmann , University of Melbourne Centre for Cancer Research John Kern Rory Kirchner , Harvard Chan Bioinformatics Core Tetiana Khotiainsteva , Ardigen Kerrin Mendler , AstraZeneca Sergey Naumenko , Harvard Chan Bioinformatics Core Jakub Nowacki , AstraZeneca John Morrissey , Harvard Chan Bioinformatics Core Lorena Pantano , Harvard Chan Bioinformatics Core Brent Pedersen , University of Colorado Denver James Porter , The University of Chicago Vlad Saveliev , Center for Algorithmic Biotechnology, St. Petersburg University Valentine Svensson , Science for Life Laboratory, Stockholm Paul Tang , UCSF Stephen Turner , University of Virginia Roman Valls , Science for Life Laboratory, Stockholm Kevin Ying , Garvan Institute of Medical Research, Sydney, Australia Steffen Möller , University of Rostock, Germany WimSpee License The code is freely available under the MIT license . About Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis bcbio-nextgen.readthedocs.io Resources Readme License MIT license Code of conduct Code of conduct Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 1k stars Watchers 87 watching Forks 355 forks Report repository Releases 14 v1.2.9 Latest Dec 15, 2021 + 13 releases Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages Python 99.0% Other 1.0% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bcbio-nextgen --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bcbio-nextgen 0.9.5 py27_1
+--------------------------
+file name   : bcbio-nextgen-0.9.5-py27_1.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.5
+build       : py27_1
+build number: 1
+size        : 1.0 MB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.5-py27_1.tar.bz2
+md5         : fb8ab3728e1fad76a55b01727b673ce2
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.6a py27_0
+---------------------------
+file name   : bcbio-nextgen-0.9.6a-py27_0.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.6a
+build       : py27_0
+build number: 0
+size        : 636 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_0.tar.bz2
+md5         : 781006b9fb52e850e982e409f03bd388
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.6a py27_1
+---------------------------
+file name   : bcbio-nextgen-0.9.6a-py27_1.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.6a
+build       : py27_1
+build number: 1
+size        : 639 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_1.tar.bz2
+md5         : ca07e2bb306fb2f4416ad1ebcade54a0
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.6a py27_2
+---------------------------
+file name   : bcbio-nextgen-0.9.6a-py27_2.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.6a
+build       : py27_2
+build number: 2
+size        : 642 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_2.tar.bz2
+md5         : a3cb1d7178e5b84fd9ecbebdbabc4460
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.6a py27_3
+---------------------------
+file name   : bcbio-nextgen-0.9.6a-py27_3.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.6a
+build       : py27_3
+build number: 3
+size        : 643 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6a-py27_3.tar.bz2
+md5         : e63b25629c3c80a106a07d6a923a3b1d
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.6 py27_0
+--------------------------
+file name   : bcbio-nextgen-0.9.6-py27_0.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.6
+build       : py27_0
+build number: 0
+size        : 655 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.6-py27_0.tar.bz2
+md5         : 2457cf1b4878bb220211b27799ab0287
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_0
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_0.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build       : py27_0
+build number: 0
+size        : 661 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_0.tar.bz2
+md5         : 5beeb479505a15b27fc1c3368f878d71
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_1
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_1.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build       : py27_1
+build number: 1
+size        : 666 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_1.tar.bz2
+md5         : 245f9508f16129a4dfc7b270cafca85a
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_2
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_2.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build       : py27_2
+build number: 2
+size        : 666 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_2.tar.bz2
+md5         : 6d85ee322f8d27092100130ea83a9711
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_3
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_3.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build       : py27_3
+build number: 3
+size        : 668 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_3.tar.bz2
+md5         : 2c38ab08340dcada3e9d2946d4e794ba
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_4
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_4.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build       : py27_4
+build number: 4
+size        : 675 KB
+license     : MIT
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bcbio-nextgen-0.9.7a-py27_4.tar.bz2
+md5         : cc54be80accf7d950b04088c69788f21
+dependencies: 
+  - arrow
+  - azure
+  - bioblend
+  - biopython
+  - boto
+  - click
+  - cython
+  - cyvcf2
+  - fabric
+  - fadapa
+  - gffutils
+  - ipyparallel
+  - ipython-cluster-helper
+  - ipywidgets
+  - joblib
+  - logbook
+  - lxml
+  - matplotlib
+  - msgpack-python
+  - nose
+  - numpy
+  - openpyxl
+  - openssl >=1.1.0,<=1.1.1
+  - pandas
+  - path.py
+  - patsy
+  - pip
+  - progressbar
+  - psutil
+  - pybedtools
+  - pycrypto
+  - pysam
+  - python 2.7*
+  - python-dateutil
+  - pyvcf
+  - pyyaml
+  - pyzmq
+  - reportlab
+  - requests
+  - scikit-learn
+  - scipy
+  - seaborn
+  - seqcluster
+  - sh
+  - sqlalchemy
+  - statsmodels
+  - tabulate
+  - toolz
+  - tornado
+
+
+bcbio-nextgen 0.9.7a py27_5
+---------------------------
+file name   : bcbio-nextgen-0.9.7a-py27_5.tar.bz2
+name        : bcbio-nextgen
+version     : 0.9.7a
+build

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bedops.manual_bundle.txt

@@ -0,0 +1,549 @@
+# Tool: bedops
+software_name: bedops
+tier: T1
+domain: t1_backfill_overall
+downloads: 235132
+summary: High-performance genomic feature operations.
+description: High-performance genomic feature operations.
+dependencies: bzip2 >=1.0.8,<2.0a0, jansson >=2.14.1,<3.0a0, libgcc >=13, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, samtools
+execution_environment: Compiled
+execution_environment_reason: inferred from native/compiled dependencies
+
+## URLs
+home_url: http://bedops.readthedocs.io
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+cli:bedops
+## CLI Help Content
+$ conda run -n bioenv_cli bedops --help
+[rc=0]
+bedops
+  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract
+            https://doi.org/10.1093/bioinformatics/bts277
+  version:  2.4.42 (typical)
+  authors:  Shane Neph & Scott Kuehn
+
+      USAGE: bedops [process-flags] <operation> <File(s)>*
+
+          Every input file must be sorted per the sort-bed utility.
+          Each operation requires a minimum number of files as shown below.
+            There is no fixed maximum number of files that may be used.
+          Input files must have at least the first 3 columns of the BED specification.
+          The program accepts BED and Starch file formats.
+          May use '-' for a file to indicate reading from standard input (BED format only).
+
+      Process Flags:
+          --chrom <chromosome> Jump to and process data for given <chromosome> only.
+          --ec                 Error check input files (slower).
+          --header             Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.
+          --help               Print this message and exit successfully.
+          --help-<operation>   Detailed help on <operation>.
+                                 An example is --help-c or --help-complement
+          --range L:R          Add 'L' bp to all start coordinates and 'R' bp to end
+                                 coordinates. Either value may be + or - to grow or
+                                 shrink regions.  With the -e/-n operations, the first
+                                 (reference) file is not padded, unlike all other files.
+          --range S            Pad or shrink input file(s) coordinates symmetrically by S.
+                                 This is shorthand for: --range -S:S.
+          --version            Print program information.
+
+      Operations: (choose one of)
+          -c, --complement [-L] File1 [File]*
+          -d, --difference ReferenceFile File2 [File]*
+          -e, --element-of [bp | percentage] ReferenceFile File2 [File]*
+                 by default, -e 100% is used.  'bedops -e 1' is also popular.
+          -i, --intersect File1 File2 [File]*
+          -m, --merge File1 [File]*
+          -n, --not-element-of [bp | percentage] ReferenceFile File2 [File]*
+                 by default, -n 100% is used.  'bedops -n 1' is also popular.
+          -p, --partition File1 [File]*
+          -s, --symmdiff File1 File2 [File]*
+          -u, --everything File1 [File]*
+          -w, --chop [bp] [--stagger <nt>] [-x] File1 [File]*
+                 by default, -w 1 is used with no staggering.
+      
+Example: bedops --range 10 -u file1.bed
+      NOTE: Only operations -e|n|u preserve all columns (no flattening)
+
+
+
+
+## URL Docs Extract
+### http://bedops.readthedocs.io
+BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit &#8212; BEDOPS v2.4.41 --> BEDOPS v2.4.41 1. Overview &rarr; Home BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit ¶ BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. You can read more about BEDOPS and how it can be useful for your research in the Overview documentation, as well as in the original manuscript . x86-64 (64-bit) binaries Installation instructions for Linux hosts Intel (64-bit, 10.10-10.15) installer package Installation instructions for Mac OS X hosts Source code (tar.gz) Source code (zip) Compilation instructions bedops - apply set operations on any number of BED inputs bedextract - efficiently extract BED features closest-features - matches nearest features between BED files bedmap - map overlapping BED elements onto target regions and optionally compute any number of common statistical operations sort-bed - apply lexicographical sort to BED data starch and unstarch - compress and extract BED data starchcat - merge compressed archives starchstrip - filter archive by chromosomes Conversion tools - convert common genomic formats to BED Parallel bam2bed and bam2starch - parallelized conversion and compression of BAM data Set operations with bedops Compression characteristics of starch Independent testing Table summary of BEDOPS toolkit Starch v2.2 format specification About nested elements Revision history Github release instructions Github repository How to install BEDOPS Usage examples of BEDOPS tools in action BEDOPS user forum BEDOPS discusssion mailing list Citation ¶ If you use BEDOPS in your research, please cite the following manuscript: Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. BEDOPS: high-performance genomic feature operations . Bioinformatics (2012) 28 (14): 1919-1920. doi: 10.1093/bioinformatics/bts277 Contents ¶ 1. Overview 1.1. About BEDOPS 1.2. Why you should use BEDOPS 1.2.1. BEDOPS tools are flexible 1.2.2. BEDOPS tools are fast and efficient 1.2.3. BEDOPS tools make your work embarrassingly easy to parallelize 1.2.4. BEDOPS tools are open, documented and supported 2. Installation 2.1. Via pre-built packages 2.1.1. Linux 2.1.2. Mac OS X 2.2. Via source code 2.2.1. Linux 2.2.2. Mac OS X 2.2.2.1. Manual compilation 2.2.2.2. Installation via Bioconda 2.2.2.3. Installation via Homebrew 2.2.3. Docker 2.2.4. Cygwin 2.3. Building an OS X installer package for redistribution 3. Revision history 3.1. Current version 3.1.1. v2.4.41 3.2. Previous versions 3.2.1. v2.4.40 3.2.2. v2.4.39 3.2.3. v2.4.38 3.2.4. v2.4.37 3.2.5. v2.4.36 3.2.6. v2.4.35 3.2.7. v2.4.34 3.2.8. v2.4.33 3.2.9. v2.4.32 3.2.10. v2.4.31 3.2.11. v2.4.30 3.2.12. v2.4.29 3.2.13. v2.4.28 3.2.14. v2.4.27 3.2.15. v2.4.26 3.2.16. v2.4.25 3.2.17. v2.4.24 3.2.18. v2.4.23 3.2.19. v2.4.22 3.2.20. v2.4.21 3.2.21. v2.4.20 3.2.22. v2.4.19 3.2.23. v2.4.18 3.2.24. v2.4.17 3.2.25. v2.4.16 3.2.26. v2.4.15 3.2.27. v2.4.14 3.2.28. v2.4.13 3.2.29. v2.4.12 3.2.30. v2.4.11 3.2.31. v2.4.10 3.2.32. v2.4.9 3.2.33. v2.4.8 3.2.34. v2.4.7 3.2.35. v2.4.6 3.2.36. v2.4.5 3.2.37. v2.4.4 3.2.38. v2.4.3 3.2.39. v2.4.2 3.2.40. v2.4.1 3.2.41. v2.4.0 3.2.42. v2.3.0 3.2.43. v2.2.0b 3.2.44. v2.2.0 3.2.45. v2.1.1 3.2.46. v2.1.0 3.2.47. v2.0.0b 3.2.48. v2.0.0a 3.2.49. v1.2.5b 3.2.50. v1.2.5 3.2.51. v1.2.3 4. Usage examples 4.1. Visualizing the relationship of SNPs and generic genomic features 4.1.1. BEDOPS tools in use 4.1.2. Script 4.1.3. Discussion 4.1.4. Downloads 4.2. Collapsing multiple BED files into a master list by signal 4.2.1. BEDOPS tools in use 4.2.2. Script 4.2.3. Discussion 4.3. Measuring the frequency of signed distances between SNPs and nearest DHSes 4.3.1. BEDOPS tools in use 4.3.2. Script 4.3.3. Discussion 4.3.4. Downloads 4.4. Finding the subset of SNPs within DHSes 4.4.1. BEDOPS tools in use 4.4.2. Script 4.4.3. Discussion 4.4.4. Downloads 4.5. Smoothing raw tag count data across the genome 4.5.1. BEDOPS tools in use 4.5.2. Script 4.6. Efficiently creating Starch-formatted archives with a cluster 4.6.1. BEDOPS tools in use 4.6.2. Script 4.6.3. Discussion 4.6.3.1. Splitting BED files 4.6.3.2. Compressing BED subsets 4.6.3.3. Stitching together compressed sets 4.7. Working with many input files at once with bedops and bedmap 4.7.1. Discussion 5. Performance 5.1. Test environment and data 5.2. Set operations with bedops 5.2.1. Direct merge (sorted) 5.2.2. Complement and intersection 5.2.3. Direct merge (unsorted) 5.2.4. Discussion 5.3. Compression characteristics of starch 5.3.1. Compression efficiency 5.3.2. Extraction time 5.4. Independent testing 5.4.1. Genomic Region Operation Kit (GROK) 5.5. Worst-case memory performance 6. Reference 6.1. Set operations 6.1.1. bedops 6.1.1.1. Inputs and outputs 6.1.1.1.1. Input 6.1.1.1.2. Output 6.1.1.2. Usage 6.1.1.3. Operations 6.1.1.3.1. Everything (-u, –everything) 6.1.1.3.2. Element-of (-e, –element-of) 6.1.1.3.3. Not-element-of (-n, –not-element-of) 6.1.1.3.4. Complement (-c, –complement) 6.1.1.3.5. Difference (-d, –difference) 6.1.1.3.6. Symmetric difference (-s, –symmdiff) 6.1.1.3.7. Intersect (-i, –intersect) 6.1.1.3.8. Merge (-m, –merge) 6.1.1.3.9. Partition (-p, –partition) 6.1.1.3.10. Chop (-w, –chop) 6.1.1.3.11. Stagger (–stagger) 6.1.1.3.12. Exclude (-x) 6.1.1.3.13. Per-chromosome operations (–chrom) 6.1.1.3.14. Range (–range) 6.1.1.4. Starch support 6.1.1.5. Error checking (–ec) 6.1.1.6. Tips 6.1.1.6.1. Chaining operations 6.1.1.6.2. Sorting inputs 6.1.2. bedextract 6.1.2.1. How it works 6.1.2.2. Inputs and outputs 6.1.2.2.1. Input 6.1.2.2.2. Output 6.1.2.3. Usage 6.1.2.3.1. Listing chromosomes 6.1.2.3.2. Retrieving elements from a specific chromosome 6.1.2.3.3. Retrieving elements which overlap target elements 6.1.2.3.3.1. What are nested elements? 6.1.2.3.3.2. Demonstration 6.1.2.4. Downloads 6.1.3. closest-features 6.1.3.1. Inputs and outputs 6.1.3.1.1. Input 6.1.3.1.2. Output 6.1.3.2. Usage 6.1.3.3. Per-chromosome operations (–chrom) 6.1.3.4. Error checking 6.1.3.5. Downloads 6.1.4. Nested elements 6.1.4.1. Definition 6.1.4.2. Example 6.1.4.3. Why nested elements matter 6.2. Statistics 6.2.1. bedmap 6.2.1.1. Inputs and outputs 6.2.1.1.1. Input 6.2.1.1.2. Output 6.2.1.2. Usage 6.2.1.3. Operations 6.2.1.3.1. Overlap criteria 6.2.1.3.1.1. Using --faster with --bp-ovr , --fraction-both , --exact or --range 6.2.1.3.2. Score operations 6.2.1.3.3. Non-score operations 6.2.1.3.3.1. Echo 6.2.1.3.3.2. Element and overlap statistics 6.2.1.3.3.3. Indicator 6.2.1.3.4. Modifiers 6.2.1.3.4.1. Range 6.2.1.3.4.2. Using --faster with --range 6.2.1.3.4.3. Formatting score output 6.2.1.3.4.4. Delimiters 6.2.1.4. I/O event handling 6.2.1.5. Per-chromosome operations (–chrom) 6.2.1.6. Starch support 6.2.1.7. Error checking 6.2.1.8. Endlines 6.2.1.9. Downloads 6.3. File management 6.3.1. Sorting 6.3.1.1. sort-bed 6.3.1.1.1. Migrating older BED and Starch files 6.3.1.1.2. Inputs and outputs 6.3.1.1.2.1. Input 6.3.1.1.2.2. Output 6.3.1.1.3. Usage 6.3.2. Compression 6.3.2.1. starch 6.3.2.1.1. Inputs and outputs 6.3.2.1.1.1. Input 6.3.2.1.1.2. Output 6.3.2.1.2. Requirements 6.3.2.1.3. Usage 6.3.2.1.4. Options 6.3.2.1.4.1. Backend compression type 6.3.2.1.4.2. Note 6.3.2.1.4.3. Per-chromosome data integrity signature 6.3.2.1.4.4. Compression progress 6.3.2.1.4.5. Headers 6.3.2.1.4.6. Unique tag 6.3.2.1.5. Example 6.3.2.2. unstarch 6.3.2.2.1. Inputs and outputs 6.3.2.2.1.1. Input 6.3.2.2.1.2. Output 6.3.2.2.2. Requirements 6.3.2.2.3. Usage 6.3.2.2.3.1. Extraction 6.3.2.2.3.2. Archive attributes 6.3.2.2.3.2.1. Metadata 6.3.2.2.3.2.2. Note 6.3.2.2.3.2.3. Timestamp 6.3.2.2.3.2.4. Compression type 6.3.2.2.3.2.5. Version 6.3.2.2.3.3. Whole-file or per-chromosome attributes 6.3.2.2.3.3.1. Data integrity 6.3.2.2.3.3.2. Elements 6.3.2.2.3.3.3. Bases 6.3.2.2.3.3.4. Duplicate element(s) 6.3.2.2.3.3.5. Nested element(s) 6.3.2.2.4. Example 6.3.2.3. starchcat 6.3.2.3.1. Parallelization 6.3.2.3.2. Inputs and outputs 6.3.2.3.2.1. Input 6.3.2.3.2.2. Output 6.3.2.3.3. Usage 6.3.2.3.3.1. Per-chromosome data integrity signature 6.3.2.3.3.2. Example 6.3.2.4. Starch (v2.x) specification 6.3.2.4.1. Archive structure 6.3.2.4.2. Magic bytes 6.3.2.4.3. Chromosome streams 6.3.2.4.4. Metadata 6.3.2.4.4.1. Data 6.3.2.4.4.1.1. Archive 6.3.2.4.4.1.2. Streams 6.3.2.4.4.2. Offset 6.3.2.4.4.3. Hash 6.3.2.4.5. Padding 6.3.2.5. starch-diff 6.3.2.5.1. Inputs and outputs 6.3.2.5.1.1. Input 6.3.2.5.1.2. Output 6.3.2.5.2. Requirements 6.3.2.5.3. Usage 6.3.3. Data conversion 6.3.3.1. convert2bed 6.3.3.1.1. Dependencies 6.3.3.1.2. Source 6.3.3.1.3. Usage 6.3.3.1.4. Example 6.3.3.2. bam2bed 6.3.3.2.1. Dependencies 6.3.3.2.2. Source 6.3.3.2.3. Usage 6.3.3.2.4. Example 6.3.3.2.5. Column mapping 6.3.3.2.6. Downloads 6.3.3.3. Parallel bam2bed 6.3.3.3.1. Dependencies 6.3.3.3.2. Source 6.3.3.3.3. Usage 6.3.3.4. Parallel bam2starch 6.3.3.4.1. Dependencies 6.3.3.4.2. Source 6.3.3.4.3. Usage 6.3.3.5. gff2bed 6.3.3.5.1. Dependencies 6.3.3.5.2. Source 6.3.3.5.3. Usage 6.3.3.5.4. Example 6.3.3.5.5. Column mapping 6.3.3.5.6. Downloads 6.3.3.6. gtf2bed 6.3.3.6.1. Dependencies 6.3.3.6.2. Source 6.3.3.6.3. Usage 6.3.3.6.4. Example 6.3.3.6.5. Column mapping 6.3.3.6.6. Downloads 6.3.3.7. gvf2bed 6.3.3.7.1. Dependencies 6.3.3.7.2. Source 6.3.3.7.3. Usage 6.3.3.7.4. Example 6.3.3.7.5. Column mapping 6.3.3.7.6. Downloads 6.3.3.8. psl2bed 6.3.3.8.1. Dependencies 6.3.3.8.2. Source 6.3.3.8.3. Usage 6.3.3.8.4. Example 6.3.3.8.5. Column mapping 6.3.3.8.6. Downloads 6.3.3.9. rmsk2bed 6.3.3.9.1. Dependencies 6.3.3.9.2. Source 6.3.3.9.3. Usage 6.3.3.9.4. Example 6.3.3.9.5. Column mapping 6.3.3.9.6. Downloads 6.3.3.10. sam2bed 6.3.3.10.1. Dependencies 6.3.3.10.2. Source 6.3.3.10.3. Usage 6.3.3.10.4. Example 6.3.3.10.5. Column mapping 6.3.3.10.6. Downloads 6.3.3.11. vcf2bed 6.3.3.11.1. Dependencies 6.3.3.11.2. Source 6.3.3.11.3. Usage 6.3.3.11.4. Customized variant handling 6.3.3.11.5. Example 6.3.3.11.6. Column mapping 6.3.3.11.7. Downloads 6.3.3.12. wig2bed 6.3.3.12.1. Source 6.3.3.12.2. Usage 6.3.3.12.3. Example 6.3.3.12.4. Downloads 7. Summary 7.1. Set operation and statistical utilities 7.1.1. bedextract 7.1.2. bedmap 7.1.3. bedops 7.1.4. closest-features 7.2. Sorting 7.2.1. sort-bed 7.3. Compression and extraction 7.3.1. starch 7.3.2. unstarch 7.3.3. starchcat 7.3.4. starchstrip 8. Release 8.1. Preparation 8.2. Release 8.3. Celebrate 9. Placeholder Table of Contents BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit Citation Contents 1. Overview &rarr; Home &copy; 2011-2022, Shane Neph, Alex Reynolds. Created using Sphinx 1.8.6 with the better theme.
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bedops --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bedops 2.4.19 0
+---------------
+file name   : bedops-2.4.19-0.tar.bz2
+name        : bedops
+version     : 2.4.19
+build       : 0
+build number: 0
+size        : 4.6 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.19-0.tar.bz2
+md5         : 45a2ac36948dea97a407cab8d1c73ee8
+dependencies: 
+  - libgcc >=4.8.2
+
+
+bedops 2.4.20 0
+---------------
+file name   : bedops-2.4.20-0.tar.bz2
+name        : bedops
+version     : 2.4.20
+build       : 0
+build number: 0
+size        : 1.3 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.20-0.tar.bz2
+md5         : 56fca9c799a7ef34c631dc582c7e9988
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.21 0
+---------------
+file name   : bedops-2.4.21-0.tar.bz2
+name        : bedops
+version     : 2.4.21
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.21-0.tar.bz2
+md5         : 5c45636d5107e58378e736ce77c94e89
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.22 0
+---------------
+file name   : bedops-2.4.22-0.tar.bz2
+name        : bedops
+version     : 2.4.22
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.22-0.tar.bz2
+md5         : ba840c1cae9e1c77e68cb0827e5d3749
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.23 0
+---------------
+file name   : bedops-2.4.23-0.tar.bz2
+name        : bedops
+version     : 2.4.23
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.23-0.tar.bz2
+md5         : bd78ca034d4033e6a6c5fdb451d01651
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.24 0
+---------------
+file name   : bedops-2.4.24-0.tar.bz2
+name        : bedops
+version     : 2.4.24
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.24-0.tar.bz2
+md5         : 5253313712f68cb95abc29e17cb1a28d
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.25 0
+---------------
+file name   : bedops-2.4.25-0.tar.bz2
+name        : bedops
+version     : 2.4.25
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.25-0.tar.bz2
+md5         : 575b6f947a7ec368d9b4056fa39fe4e5
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.26 0
+---------------
+file name   : bedops-2.4.26-0.tar.bz2
+name        : bedops
+version     : 2.4.26
+build       : 0
+build number: 0
+size        : 1.5 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.26-0.tar.bz2
+md5         : 36f3ce13a04d1639ce66bd1e2bc6cdd4
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.27 0
+---------------
+file name   : bedops-2.4.27-0.tar.bz2
+name        : bedops
+version     : 2.4.27
+build       : 0
+build number: 0
+size        : 2.2 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.27-0.tar.bz2
+md5         : b809e57e15b4dbc67dc9e73d9995c6ab
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.30 0
+---------------
+file name   : bedops-2.4.30-0.tar.bz2
+name        : bedops
+version     : 2.4.30
+build       : 0
+build number: 0
+size        : 2.2 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.30-0.tar.bz2
+md5         : 2577e9299989c0886e89713c73875988
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.32 0
+---------------
+file name   : bedops-2.4.32-0.tar.bz2
+name        : bedops
+version     : 2.4.32
+build       : 0
+build number: 0
+size        : 8.4 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.32-0.tar.bz2
+md5         : 242f39dfcba1c3805142e764f9c420b4
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.33 0
+---------------
+file name   : bedops-2.4.33-0.tar.bz2
+name        : bedops
+version     : 2.4.33
+build       : 0
+build number: 0
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+license     : GPLv2
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+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.33-0.tar.bz2
+md5         : 52f9d6af93722b287ba8409a1ddbdfb1
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.34 0
+---------------
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+name        : bedops
+version     : 2.4.34
+build       : 0
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+license     : GPLv2
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+md5         : 89aa273e077a73916c64631967c3404c
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.35 0
+---------------
+file name   : bedops-2.4.35-0.tar.bz2
+name        : bedops
+version     : 2.4.35
+build       : 0
+build number: 0
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+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-0.tar.bz2
+md5         : d78241332e704e13466424af6278e9c3
+dependencies: 
+  - libgcc
+
+
+bedops 2.4.35 h2d50403_1
+------------------------
+file name   : bedops-2.4.35-h2d50403_1.tar.bz2
+name        : bedops
+version     : 2.4.35
+build       : h2d50403_1
+build number: 1
+size        : 8.3 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-h2d50403_1.tar.bz2
+md5         : d029e15fc2eae7953e1f52697f27b713
+timestamp   : 2018-07-03 07:27:11 UTC
+dependencies: 
+  - libstdcxx-ng >=4.9
+
+
+bedops 2.4.35 h6bb024c_2
+------------------------
+file name   : bedops-2.4.35-h6bb024c_2.tar.bz2
+name        : bedops
+version     : 2.4.35
+build       : h6bb024c_2
+build number: 2
+size        : 8.9 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.35-h6bb024c_2.tar.bz2
+md5         : 14c8863bd833cfcc7a1bd4860bc613ec
+timestamp   : 2019-04-26 08:22:16 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+
+
+bedops 2.4.36 h6bb024c_0
+------------------------
+file name   : bedops-2.4.36-h6bb024c_0.tar.bz2
+name        : bedops
+version     : 2.4.36
+build       : h6bb024c_0
+build number: 0
+size        : 9.1 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.36-h6bb024c_0.tar.bz2
+md5         : 53a29db402c962ad05ca2672c35a74ac
+timestamp   : 2019-05-03 22:03:43 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+
+
+bedops 2.4.36 h6bb024c_1
+------------------------
+file name   : bedops-2.4.36-h6bb024c_1.tar.bz2
+name        : bedops
+version     : 2.4.36
+build       : h6bb024c_1
+build number: 1
+size        : 9.0 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.36-h6bb024c_1.tar.bz2
+md5         : 0025cfb4a95a2bd0702aa4748fc17604
+timestamp   : 2019-05-22 02:53:52 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - samtools
+
+
+bedops 2.4.37 hc9558a2_0
+------------------------
+file name   : bedops-2.4.37-hc9558a2_0.tar.bz2
+name        : bedops
+version     : 2.4.37
+build       : hc9558a2_0
+build number: 0
+size        : 9.0 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.37-hc9558a2_0.tar.bz2
+md5         : aab6f7123b4f0f20e20a9391527d2fa9
+timestamp   : 2019-10-12 05:30:59 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - samtools
+
+
+bedops 2.4.38 hc9558a2_0
+------------------------
+file name   : bedops-2.4.38-hc9558a2_0.tar.bz2
+name        : bedops
+version     : 2.4.38
+build       : hc9558a2_0
+build number: 0
+size        : 9.0 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.38-hc9558a2_0.tar.bz2
+md5         : 1bc8cbe7d8ff717e30e255e7c18cd16c
+timestamp   : 2020-04-02 07:44:05 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - samtools
+
+
+bedops 2.4.39 h7d875b9_1
+------------------------
+file name   : bedops-2.4.39-h7d875b9_1.tar.bz2
+name        : bedops
+version     : 2.4.39
+build       : h7d875b9_1
+build number: 1
+size        : 9.7 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.39-h7d875b9_1.tar.bz2
+md5         : d35bd7b8e442e99930492f3cab1129d8
+timestamp   : 2021-04-01 10:49:55 UTC
+dependencies: 
+  - libgcc-ng >=9.3.0
+  - libstdcxx-ng >=9.3.0
+  - samtools
+
+
+bedops 2.4.39 hc9558a2_0
+------------------------
+file name   : bedops-2.4.39-hc9558a2_0.tar.bz2
+name        : bedops
+version     : 2.4.39
+build       : hc9558a2_0
+build number: 0
+size        : 9.1 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.39-hc9558a2_0.tar.bz2
+md5         : ba1187bd8b16aa332fc9949158970d20
+timestamp   : 2020-04-07 08:32:36 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - samtools
+
+
+bedops 2.4.40 h9f5acd7_0
+------------------------
+file name   : bedops-2.4.40-h9f5acd7_0.tar.bz2
+name        : bedops
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+build       : h9f5acd7_0
+build number: 0
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+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.40-h9f5acd7_0.tar.bz2
+md5         : 6defd1d9128821c714212a7bc4ff82bf
+timestamp   : 2022-07-04 14:24:58 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+  - samtools
+
+
+bedops 2.4.41 h4ac6f70_1
+------------------------
+file name   : bedops-2.4.41-h4ac6f70_1.tar.bz2
+name        : bedops
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+build       : h4ac6f70_1
+build number: 1
+size        : 10.6 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h4ac6f70_1.tar.bz2
+md5         : e5f26003751720877b5a157c6c490834
+timestamp   : 2023-05-27 22:31:16 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+  - samtools
+
+
+bedops 2.4.41 h4ac6f70_2
+------------------------
+file name   : bedops-2.4.41-h4ac6f70_2.tar.bz2
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+build       : h4ac6f70_2
+build number: 2
+size        : 10.5 MB
+license     : GPLv2
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+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h4ac6f70_2.tar.bz2
+md5         : bc0c400539a8809589b3f2584a07571e
+timestamp   : 2024-03-20 10:32:49 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+  - samtools
+
+
+bedops 2.4.41 h9948957_3
+------------------------
+file name   : bedops-2.4.41-h9948957_3.tar.bz2
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+build       : h9948957_3
+build number: 3
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+md5         : 686bffd5fe7d8935465d79627ff655e6
+timestamp   : 2024-12-15 18:16:28 UTC
+dependencies: 
+  - libgcc >=13
+  - libstdcxx >=13
+  - samtools
+
+
+bedops 2.4.41 h9f5acd7_0
+------------------------
+file name   : bedops-2.4.41-h9f5acd7_0.tar.bz2
+name        : bedops
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+build       : h9f5acd7_0
+build number: 0
+size        : 10.7 MB
+license     : GPLv2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bedops-2.4.41-h9f5acd7_0.tar.bz2
+md5         : 19912c6cd12e4d66cea791ae905ed4f4
+timestamp   : 2022-07-14 09:09:14 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libstdcxx-ng >=12
+  - samtools
+
+
+bedops 2.

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/biobambam.manual_bundle.txt

@@ -0,0 +1,456 @@
+# Tool: biobambam
+software_name: biobambam
+tier: T1
+domain: t1_backfill_overall
+downloads: 119590
+summary: Tools for early stage alignment file processing.
+description: Tools for early stage alignment file processing.
+dependencies: gmp >=6.3.0,<7.0a0, libgcc >=13, libmaus2 >=2.0.813, libmaus2 >=2.0.813,<3.0a0, libstdcxx >=13, libzlib >=1.3.1,<2.0a0, xerces-c >=3.2.5,<3.3.0a0
+execution_environment: Compiled
+execution_environment_reason: inferred from native/compiled dependencies
+
+## URLs
+home_url: https://gitlab.com/german.tischler/biobambam2
+doc_url: 
+dev_url: https://gitlab.com/german.tischler/biobambam2
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge biobambam --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+biobambam 2.0.25 0
+------------------
+file name   : biobambam-2.0.25-0.tar.bz2
+name        : biobambam
+version     : 2.0.25
+build       : 0
+build number: 0
+size        : 13.7 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.25-0.tar.bz2
+md5         : 46a37f9e889c3865bf64f9404a1ac9e5
+dependencies: []
+
+
+biobambam 2.0.39 0
+------------------
+file name   : biobambam-2.0.39-0.tar.bz2
+name        : biobambam
+version     : 2.0.39
+build       : 0
+build number: 0
+size        : 15.0 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.39-0.tar.bz2
+md5         : 4a860111d249d61da98d1d7733bb227d
+dependencies: []
+
+
+biobambam 2.0.42 0
+------------------
+file name   : biobambam-2.0.42-0.tar.bz2
+name        : biobambam
+version     : 2.0.42
+build       : 0
+build number: 0
+size        : 15.3 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.42-0.tar.bz2
+md5         : 26b76d132cfdb17b1d1735f9f0392397
+dependencies: []
+
+
+biobambam 2.0.44 0
+------------------
+file name   : biobambam-2.0.44-0.tar.bz2
+name        : biobambam
+version     : 2.0.44
+build       : 0
+build number: 0
+size        : 15.4 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.44-0.tar.bz2
+md5         : 1d3f23fff5c8fd5cd59ffe0119b814d9
+dependencies: []
+
+
+biobambam 2.0.57 0
+------------------
+file name   : biobambam-2.0.57-0.tar.bz2
+name        : biobambam
+version     : 2.0.57
+build       : 0
+build number: 0
+size        : 16.1 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.57-0.tar.bz2
+md5         : 6967c1e021c9d9c3ca3bc6fcb3ba9478
+dependencies: []
+
+
+biobambam 2.0.58 0
+------------------
+file name   : biobambam-2.0.58-0.tar.bz2
+name        : biobambam
+version     : 2.0.58
+build       : 0
+build number: 0
+size        : 15.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.58-0.tar.bz2
+md5         : 6cf8c090e46eaa549e71713cf8a415f1
+dependencies: []
+
+
+biobambam 2.0.62 0
+------------------
+file name   : biobambam-2.0.62-0.tar.bz2
+name        : biobambam
+version     : 2.0.62
+build       : 0
+build number: 0
+size        : 16.0 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.62-0.tar.bz2
+md5         : 4a1a4090e419586af76ee06e1aaeedc2
+dependencies: []
+
+
+biobambam 2.0.72 0
+------------------
+file name   : biobambam-2.0.72-0.tar.bz2
+name        : biobambam
+version     : 2.0.72
+build       : 0
+build number: 0
+size        : 16.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.72-0.tar.bz2
+md5         : 5bebc593b1495e1779a9ed583f953304
+dependencies: []
+
+
+biobambam 2.0.78 0
+------------------
+file name   : biobambam-2.0.78-0.tar.bz2
+name        : biobambam
+version     : 2.0.78
+build       : 0
+build number: 0
+size        : 17.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.78-0.tar.bz2
+md5         : b13650d85c8c7dc87c84973822f0cf40
+dependencies: []
+
+
+biobambam 2.0.79 0
+------------------
+file name   : biobambam-2.0.79-0.tar.bz2
+name        : biobambam
+version     : 2.0.79
+build       : 0
+build number: 0
+size        : 19.1 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.79-0.tar.bz2
+md5         : 1209b6394291f1063c18fd8e8d1d4549
+dependencies: []
+
+
+biobambam 2.0.87 0
+------------------
+file name   : biobambam-2.0.87-0.tar.bz2
+name        : biobambam
+version     : 2.0.87
+build       : 0
+build number: 0
+size        : 19.1 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-0.tar.bz2
+md5         : 87a150ed26a8edda38ba021b1fe29b79
+dependencies: []
+
+
+biobambam 2.0.87 1
+------------------
+file name   : biobambam-2.0.87-1.tar.bz2
+name        : biobambam
+version     : 2.0.87
+build       : 1
+build number: 1
+size        : 19.1 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-1.tar.bz2
+md5         : 1ddb0afcd9fc7c3b1349eda278beba86
+timestamp   : 2018-07-03 02:20:40 UTC
+dependencies: []
+
+
+biobambam 2.0.87 h516909a_2
+---------------------------
+file name   : biobambam-2.0.87-h516909a_2.tar.bz2
+name        : biobambam
+version     : 2.0.87
+build       : h516909a_2
+build number: 2
+size        : 18.8 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.87-h516909a_2.tar.bz2
+md5         : 54c29e929e8215a33ef7d5546b88bea7
+timestamp   : 2020-08-13 11:13:48 UTC
+dependencies: 
+  - libgcc-ng >=7.5.0
+
+
+biobambam 2.0.179 h7d875b9_1
+----------------------------
+file name   : biobambam-2.0.179-h7d875b9_1.tar.bz2
+name        : biobambam
+version     : 2.0.179
+build       : h7d875b9_1
+build number: 1
+size        : 22.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.179-h7d875b9_1.tar.bz2
+md5         : 56669f8ee6c5d01eddd3118a6911815f
+timestamp   : 2021-03-28 09:17:56 UTC
+dependencies: 
+  - libgcc-ng >=9.3.0
+  - libmaus2
+  - libstdcxx-ng >=9.3.0
+
+
+biobambam 2.0.179 hc9558a2_0
+----------------------------
+file name   : biobambam-2.0.179-hc9558a2_0.tar.bz2
+name        : biobambam
+version     : 2.0.179
+build       : hc9558a2_0
+build number: 0
+size        : 19.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.179-hc9558a2_0.tar.bz2
+md5         : 807e5ec9d83a0a0845ba349f44d3d384
+timestamp   : 2021-03-12 16:28:18 UTC
+dependencies: 
+  - libgcc-ng >=7.5.0
+  - libmaus2
+  - libstdcxx-ng >=7.5.0
+
+
+biobambam 2.0.180 h7d875b9_1
+----------------------------
+file name   : biobambam-2.0.180-h7d875b9_1.tar.bz2
+name        : biobambam
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+build       : h7d875b9_1
+build number: 1
+size        : 22.9 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.180-h7d875b9_1.tar.bz2
+md5         : 8c73a7a009740bafbe01b8f267ae76ba
+timestamp   : 2021-03-31 22:32:24 UTC
+dependencies: 
+  - libgcc-ng >=9.3.0
+  - libmaus2 >=2.0.774
+  - libstdcxx-ng >=9.3.0
+
+
+biobambam 2.0.180 hc9558a2_0
+----------------------------
+file name   : biobambam-2.0.180-hc9558a2_0.tar.bz2
+name        : biobambam
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+build       : hc9558a2_0
+build number: 0
+size        : 21.1 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.180-hc9558a2_0.tar.bz2
+md5         : 9d9b0101709ab1dcecc93b3219b63938
+timestamp   : 2021-03-24 10:51:44 UTC
+dependencies: 
+  - libgcc-ng >=7.5.0
+  - libmaus2 >=2.0.774
+  - libstdcxx-ng >=7.5.0
+
+
+biobambam 2.0.182 h7d875b9_0
+----------------------------
+file name   : biobambam-2.0.182-h7d875b9_0.tar.bz2
+name        : biobambam
+version     : 2.0.182
+build       : h7d875b9_0
+build number: 0
+size        : 22.8 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.182-h7d875b9_0.tar.bz2
+md5         : ea5aec9969d6f922522cee0976e4feff
+timestamp   : 2021-04-21 13:03:34 UTC
+dependencies: 
+  - libgcc-ng >=9.3.0
+  - libmaus2 >=2.0.777
+  - libstdcxx-ng >=9.3.0
+
+
+biobambam 2.0.182 h9f5acd7_1
+----------------------------
+file name   : biobambam-2.0.182-h9f5acd7_1.tar.bz2
+name        : biobambam
+version     : 2.0.182
+build       : h9f5acd7_1
+build number: 1
+size        : 21.2 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.182-h9f5acd7_1.tar.bz2
+md5         : 4d249b4b666cf4b011ad1259c5d275ab
+timestamp   : 2022-02-23 11:30:46 UTC
+dependencies: 
+  - libgcc-ng >=10.3.0
+  - libmaus2 >=2.0.777
+  - libstdcxx-ng >=10.3.0
+
+
+biobambam 2.0.183 h4ac6f70_3
+----------------------------
+file name   : biobambam-2.0.183-h4ac6f70_3.tar.bz2
+name        : biobambam
+version     : 2.0.183
+build       : h4ac6f70_3
+build number: 3
+size        : 21.2 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h4ac6f70_3.tar.bz2
+md5         : 679768a5b2b79a198cc0a57e4ac427d2
+timestamp   : 2023-05-17 06:52:43 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libmaus2 >=2.0.810,<2.1.0a0
+  - libstdcxx-ng >=12
+
+
+biobambam 2.0.183 h4ac6f70_4
+----------------------------
+file name   : biobambam-2.0.183-h4ac6f70_4.tar.bz2
+name        : biobambam
+version     : 2.0.183
+build       : h4ac6f70_4
+build number: 4
+size        : 21.3 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h4ac6f70_4.tar.bz2
+md5         : b440f7302f8b51b1747a51a046a35c4c
+timestamp   : 2024-04-18 05:45:57 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libmaus2 >=2.0.810,<2.1.0a0
+  - libstdcxx-ng >=12
+
+
+biobambam 2.0.183 h9f5acd7_0
+----------------------------
+file name   : biobambam-2.0.183-h9f5acd7_0.tar.bz2
+name        : biobambam
+version     : 2.0.183
+build       : h9f5acd7_0
+build number: 0
+size        : 21.3 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_0.tar.bz2
+md5         : 46ec04b1b6cdac24dc886291dd5231b9
+timestamp   : 2022-03-04 10:29:53 UTC
+dependencies: 
+  - libgcc-ng >=10.3.0
+  - libmaus2 >=2.0.810
+  - libstdcxx-ng >=10.3.0
+
+
+biobambam 2.0.183 h9f5acd7_1
+----------------------------
+file name   : biobambam-2.0.183-h9f5acd7_1.tar.bz2
+name        : biobambam
+version     : 2.0.183
+build       : h9f5acd7_1
+build number: 1
+size        : 21.3 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_1.tar.bz2
+md5         : be69d68d770f4f093a7399adad8ef994
+timestamp   : 2022-03-12 10:02:19 UTC
+dependencies: 
+  - libgcc-ng >=10.3.0
+  - libmaus2 >=2.0.810
+  - libstdcxx-ng >=10.3.0
+
+
+biobambam 2.0.183 h9f5acd7_2
+----------------------------
+file name   : biobambam-2.0.183-h9f5acd7_2.tar.bz2
+name        : biobambam
+version     : 2.0.183
+build       : h9f5acd7_2
+build number: 2
+size        : 21.2 MB
+license     : GPLv3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h9f5acd7_2.tar.bz2
+md5         : 2f65c8ca2ee49978c66201aa1b292781
+timestamp   : 2022-08-09 14:44:50 UTC
+dependencies: 
+  - libgcc-ng >=12
+  - libmaus2 >=2.0.810,<2.1.0a0
+  - libstdcxx-ng >=12
+
+
+biobambam 2.0.185 h02148a2_0
+----------------------------
+file name   : biobambam-2.0.185-h02148a2_0.tar.bz2
+name        : biobambam
+version     : 2.0.185
+build       : h02148a2_0
+build number: 0
+size        : 21.3 MB
+license     : GPL-3.0-or-later
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.185-h02148a2_0.tar.bz2
+md5         : aaa114d0dc3f75f6984cdcd32f4ebe9c
+timestamp   : 2024-11-18 10:15:06 UTC
+dependencies: 
+  - gmp >=6.3.0,<7.0a0
+  - libgcc >=12
+  - libmaus2 >=2.0.813
+  - libmaus2 >=2.0.813,<3.0a0
+  - libstdcxx >=12
+  - libzlib >=1.2.13,<2.0a0
+  - xerces-c >=3.2.5,<3.3.0a0
+
+
+biobambam 2.0.185 h85de650_1
+----------------------------
+file name   : biobambam-2.0.185-h85de650_1.tar.bz2
+name        : biobambam
+version     : 2.0.185

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-alabaster.sfe.manual_bundle.txt

@@ -0,0 +1,56 @@
+# Tool: bioconductor-alabaster.sfe
+software_name: bioconductor-alabaster.sfe
+tier: T1
+domain: spatial_transcriptomics
+downloads: 32
+summary: Language agnostic on disk serialization of SpatialFeatureExperiment
+description: Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment.
+dependencies: bioconductor-alabaster.base >=1.10.0,<1.11.0, bioconductor-alabaster.sce >=1.10.0,<1.11.0, bioconductor-alabaster.spatial >=1.10.0,<1.11.0, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-rbioformats >=1.10.0,<1.11.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-jsonlite, r-sfarrow, r-spatialreg, r-spdep, r-terra, r-xml2
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/alabaster.sfe.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/alabaster.sfe.html
+Bioconductor - alabaster.sfe Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages alabaster.sfe alabaster.sfe This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see alabaster.sfe . Language agnostic on disk serialization of SpatialFeatureExperiment DOI: 10.18129/B9.bioc.alabaster.sfe Bioconductor version: 3.22 Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment. Author: Lambda Moses [aut, cre] ORCID: 0000-0002-7092-9427 Maintainer: Lambda Moses &#x3c;&#x64;&#x6c;&#x33;&#x37;&#x36;&#x34;&#x20;&#x61;&#x74;&#x20;&#x63;&#x6f;&#x6c;&#x75;&#x6d;&#x62;&#x69;&#x61;&#x2e;&#x65;&#x64;&#x75;&#x3e; Citation (from within R, enter citation("alabaster.sfe") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("alabaster.sfe") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("alabaster.sfe") Overview HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Software , Spatial Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License MIT + file LICENSE Depends R (>= 4.1.0), SpatialFeatureExperiment (>= 1.9.3), alabaster.base Imports alabaster.sce , alabaster.spatial (>= 1.5.2), EBImage , jsonlite , methods, RBioFormats , S4Vectors , sfarrow , SingleCellExperiment , spatialreg , spdep , SummarizedExperiment , terra , xml2 System Requirements URL https://pachterlab.github.io/alabaster.sfe/ Bug Reports https://github.com/pachterlab/alabaster.sfe/issues See More Suggests BiocStyle , fs , knitr , rmarkdown , scater , sf , SFEData , testthat (>= 3.0.0), Voyager (>= 1.9.1) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package alabaster.sfe_1.2.0.tar.gz Windows Binary (x86_64) alabaster.sfe_1.2.0.zip macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/alabaster.sfe Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/alabaster.sfe Bioc Package Browser https://code.bioconductor.org/browse/alabaster.sfe/ Package Short Url https://bioconductor.org/packages/alabaster.sfe/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-alabaster.sfe --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-alabaster.sfe 1.2.0 r45hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-alabaster.sfe-1.2.0-r45hdfd78af_0.conda
+name        : bioconductor-alabaster.sfe
+version     : 1.2.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 2.8 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-alabaster.sfe-1.2.0-r45hdfd78af_0.conda
+md5         : 779ed397cda34addebaef28746554e9e
+timestamp   : 2026-03-15 00:28:16 UTC
+dependencies: 
+  - bioconductor-alabaster.base >=1.10.0,<1.11.0
+  - bioconductor-alabaster.sce >=1.10.0,<1.11.0
+  - bioconductor-alabaster.spatial >=1.10.0,<1.11.0
+  - bioconductor-ebimage >=4.52.0,<4.53.0
+  - bioconductor-rbioformats >=1.10.0,<1.11.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialfeatureexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-base >=4.5,<4.6.0a0
+  - r-jsonlite
+  - r-sfarrow
+  - r-spatialreg
+  - r-spdep
+  - r-terra
+  - r-xml2

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-banksy.manual_bundle.txt

@@ -0,0 +1,60 @@
+# Tool: bioconductor-banksy
+software_name: bioconductor-banksy
+tier: T1
+domain: spatial_transcriptomics
+downloads: 66
+summary: Spatial transcriptomic clustering
+description: Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-genomeinfodb >=1.46.0,<1.47.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-aricode, r-base >=4.5,<4.6.0a0, r-data.table, r-dbscan, r-igraph, r-irlba, r-leidenalg >=1.1.0, r-matrix, r-mclust, r-rcpphungarian, r-uwot
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/Banksy.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/Banksy.html
+Bioconductor - Banksy Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Banksy Banksy This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Banksy . Spatial transcriptomic clustering DOI: 10.18129/B9.bioc.Banksy Bioconductor version: 3.22 Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation. Author: Vipul Singhal [aut], Joseph Lee [aut, cre] ORCID: 0000-0002-4983-4714 Maintainer: Joseph Lee &#x3c;&#x6a;&#x6f;&#x73;&#x65;&#x70;&#x68;&#x2e;&#x6c;&#x65;&#x65;&#x20;&#x61;&#x74;&#x20;&#x75;&#x2e;&#x6e;&#x75;&#x73;&#x2e;&#x65;&#x64;&#x75;&#x3e; Citation (from within R, enter citation("Banksy") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Banksy") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Banksy") Domain segmentation (STARmap PLUS mouse brain) HTML R Script Multi-sample analysis (10x Visium Human DLPFC) HTML R Script Parameter selection (VeraFISH Mouse Hippocampus) HTML R Script Spatial data integration with Harmony (10x Visium Human DLPFC) HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , DimensionReduction , GeneExpression , SingleCell , Software , Spatial Version 1.6.0 In Bioconductor since BioC 3.19 (R-4.4) (2 years) License file LICENSE Depends R (>= 4.4.0) Imports aricode , BiocParallel , data.table , dbscan , SpatialExperiment , SingleCellExperiment , SummarizedExperiment , S4Vectors , stats, Matrix , MatrixGenerics , mclust , igraph , irlba , leidenAlg (>= 1.1.0), utils, uwot , RcppHungarian , GenomeInfoDb System Requirements URL https://github.com/prabhakarlab/Banksy Bug Reports https://github.com/prabhakarlab/Banksy/issues See More Suggests knitr , rmarkdown , pals , scuttle , scater , scran , cowplot , ggplot2 , testthat (>= 3.0.0), harmony , Seurat , ExperimentHub , spatialLIBD , BiocStyle Linking To Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Banksy_1.6.0.tar.gz Windows Binary (x86_64) Banksy_1.6.0.zip (64-bit only) macOS Binary (x86_64) Banksy_1.6.0.tgz macOS Binary (arm64) Banksy_1.6.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Banksy Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Banksy Bioc Package Browser https://code.bioconductor.org/browse/Banksy/ Package Short Url https://bioconductor.org/packages/Banksy/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-banksy --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-banksy 1.6.0 r45hdfd78af_0
+---------------------------------------
+file name   : bioconductor-banksy-1.6.0-r45hdfd78af_0.conda
+name        : bioconductor-banksy
+version     : 1.6.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 3.1 MB
+license     : file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-banksy-1.6.0-r45hdfd78af_0.conda
+md5         : de8878bdca7f4846adba7a5b97440f2a
+timestamp   : 2026-03-15 00:05:11 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-genomeinfodb >=1.46.0,<1.47.0
+  - bioconductor-matrixgenerics >=1.22.0,<1.23.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-aricode
+  - r-base >=4.5,<4.6.0a0
+  - r-data.table
+  - r-dbscan
+  - r-igraph
+  - r-irlba
+  - r-leidenalg >=1.1.0
+  - r-matrix
+  - r-mclust
+  - r-rcpphungarian
+  - r-uwot

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-benchdamic.manual_bundle.txt

@@ -0,0 +1,145 @@
+# Tool: bioconductor-benchdamic
+software_name: bioconductor-benchdamic
+tier: T1
+domain: single_cell
+downloads: 6358
+summary: Benchmark of differential abundance methods on microbiome data
+description: Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
+dependencies: bioconductor-aldex2 >=1.32.0,<1.33.0, bioconductor-ancombc >=2.2.0,<2.3.0, bioconductor-biocparallel >=1.34.0,<1.35.0, bioconductor-dearseq >=1.12.0,<1.13.0, bioconductor-deseq2 >=1.40.0,<1.41.0, bioconductor-edger >=3.42.0,<3.43.0, bioconductor-limma >=3.56.0,<3.57.0, bioconductor-mast >=1.26.0,<1.27.0, bioconductor-metagenomeseq >=1.42.0,<1.43.0, bioconductor-noiseq >=2.44.0,<2.45.0, bioconductor-phyloseq >=1.44.0,<1.45.0, bioconductor-summarizedexperiment >=1.30.0,<1.31.0, bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0, bioconductor-zinbwave >=1.22.0,<1.23.0, r-base >=4.3,<4.4.0a0, r-corncob, r-cowplot, r-ggdendro, r-ggplot2, r-ggridges, r-lme4, r-mglm, r-plyr, r-rcolorbrewer, r-reshape2, r-seurat, r-tidytext
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.14/bioc/html/benchdamic.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.14/bioc/html/benchdamic.html
+Bioconductor - benchdamic About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages benchdamic benchdamic This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see benchdamic . Benchmark of differential abundance methods on microbiome data DOI: 10.18129/B9.bioc.benchdamic Bioconductor version: 3.14 Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization. Author: Matteo Calgaro [aut, cre] Maintainer: Matteo Calgaro &#x3c;&#x6d;&#x63;&#x61;&#x6c;&#x67;&#x61;&#x72;&#x6f;&#x39;&#x33;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("benchdamic") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("benchdamic") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("benchdamic") Intro HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , Metagenomics , Microbiome , MultipleComparison , Normalization , Preprocessing , Software Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License Artistic-2.0 Depends R (>= 4.1.0) Imports stats, stats4, utils, methods, phyloseq , BiocParallel , zinbwave , edgeR , DESeq2 , limma , ALDEx2 , corncob, SummarizedExperiment , MAST , Seurat, metagenomeSeq , MGLM, ggplot2, RColorBrewer, plyr, ffpe , reshape2, ggdendro, graphics, cowplot System Requirements URL Bug Reports https://github.com/mcalgaro93/benchdamic/issues See More Suggests knitr, rmarkdown, HMP16SData , curatedMetagenomicData , BiocStyle , testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package benchdamic_1.0.0.tar.gz Windows Binary benchdamic_1.0.0.zip macOS 10.13 (High Sierra) benchdamic_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/benchdamic Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/benchdamic Bioc Package Browser https://code.bioconductor.org/browse/benchdamic/ Package Short Url https://bioconductor.org/packages/benchdamic/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-benchdamic --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-benchdamic 1.0.0 r41hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-benchdamic-1.0.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-benchdamic
+version     : 1.0.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 2.2 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.0.0-r41hdfd78af_0.tar.bz2
+md5         : 4d364ff15ef0429072343cf194e0c58c
+timestamp   : 2021-11-11 08:58:48 UTC
+dependencies: 
+  - bioconductor-aldex2 >=1.26.0,<1.27.0
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - bioconductor-deseq2 >=1.34.0,<1.35.0
+  - bioconductor-edger >=3.36.0,<3.37.0
+  - bioconductor-ffpe >=1.38.0,<1.39.0
+  - bioconductor-limma >=3.50.0,<3.51.0
+  - bioconductor-mast >=1.20.0,<1.21.0
+  - bioconductor-metagenomeseq >=1.36.0,<1.37.0
+  - bioconductor-phyloseq >=1.38.0,<1.39.0
+  - bioconductor-summarizedexperiment >=1.24.0,<1.25.0
+  - bioconductor-zinbwave >=1.16.0,<1.17.0
+  - r-base >=4.1,<4.2.0a0
+  - r-corncob
+  - r-cowplot
+  - r-ggdendro
+  - r-ggplot2
+  - r-mglm
+  - r-plyr
+  - r-rcolorbrewer
+  - r-reshape2
+  - r-seurat
+
+
+bioconductor-benchdamic 1.4.0 r42hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-benchdamic-1.4.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-benchdamic
+version     : 1.4.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 4.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.4.0-r42hdfd78af_0.tar.bz2
+md5         : 006319896db140041670bca30798be68
+timestamp   : 2022-11-10 04:38:45 UTC
+dependencies: 
+  - bioconductor-aldex2 >=1.30.0,<1.31.0
+  - bioconductor-ancombc >=2.0.0,<2.1.0
+  - bioconductor-biocparallel >=1.32.0,<1.33.0
+  - bioconductor-dearseq >=1.10.0,<1.11.0
+  - bioconductor-deseq2 >=1.38.0,<1.39.0
+  - bioconductor-edger >=3.40.0,<3.41.0
+  - bioconductor-limma >=3.54.0,<3.55.0
+  - bioconductor-mast >=1.24.0,<1.25.0
+  - bioconductor-metagenomeseq >=1.40.0,<1.41.0
+  - bioconductor-noiseq >=2.42.0,<2.43.0
+  - bioconductor-phyloseq >=1.42.0,<1.43.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - bioconductor-treesummarizedexperiment >=2.6.0,<2.7.0
+  - bioconductor-zinbwave >=1.20.0,<1.21.0
+  - r-base >=4.2,<4.3.0a0
+  - r-corncob
+  - r-cowplot
+  - r-ggdendro
+  - r-ggplot2
+  - r-ggridges
+  - r-mglm
+  - r-plyr
+  - r-rcolorbrewer
+  - r-reshape2
+  - r-seurat
+  - r-tidytext
+
+
+bioconductor-benchdamic 1.6.0 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-benchdamic-1.6.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-benchdamic
+version     : 1.6.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 4.2 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-benchdamic-1.6.0-r43hdfd78af_0.tar.bz2
+md5         : 3edf7c67ea4255d0908c4687651e2950
+timestamp   : 2023-07-18 16:51:05 UTC
+dependencies: 
+  - bioconductor-aldex2 >=1.32.0,<1.33.0
+  - bioconductor-ancombc >=2.2.0,<2.3.0
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-dearseq >=1.12.0,<1.13.0
+  - bioconductor-deseq2 >=1.40.0,<1.41.0
+  - bioconductor-edger >=3.42.0,<3.43.0
+  - bioconductor-limma >=3.56.0,<3.57.0
+  - bioconductor-mast >=1.26.0,<1.27.0
+  - bioconductor-metagenomeseq >=1.42.0,<1.43.0
+  - bioconductor-noiseq >=2.44.0,<2.45.0
+  - bioconductor-phyloseq >=1.44.0,<1.45.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - bioconductor-treesummarizedexperiment >=2.8.0,<2.9.0
+  - bioconductor-zinbwave >=1.22.0,<1.23.0
+  - r-base >=4.3,<4.4.0a0
+  - r-corncob
+  - r-cowplot
+  - r-ggdendro
+  - r-ggplot2
+  - r-ggridges
+  - r-lme4
+  - r-mglm
+  - r-plyr
+  - r-rcolorbrewer
+  - r-reshape2
+  - r-seurat
+  - r-tidytext

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biocbaseutils.manual_bundle.txt

@@ -0,0 +1,108 @@
+# Tool: bioconductor-biocbaseutils
+software_name: bioconductor-biocbaseutils
+tier: T1
+domain: t1_backfill_overall
+downloads: 185514
+summary: General utility functions for developing Bioconductor packages
+description: The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem.
+dependencies: r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.16/bioc/html/BiocBaseUtils.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.16/bioc/html/BiocBaseUtils.html
+Bioconductor - BiocBaseUtils About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages BiocBaseUtils BiocBaseUtils This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BiocBaseUtils . General utility functions for developing Bioconductor packages DOI: 10.18129/B9.bioc.BiocBaseUtils Bioconductor version: 3.16 The package provides utility functions related to package development. These include functions that replace slots, and selectors for show methods. It aims to coalesce the various helper functions often re-used throughout the Bioconductor ecosystem. Author: Marcel Ramos [aut, cre] , Martin Morgan [ctb], Hervé Pagès [ctb] Maintainer: Marcel Ramos &#x3c;&#x6d;&#x61;&#x72;&#x63;&#x65;&#x6c;&#x2e;&#x72;&#x61;&#x6d;&#x6f;&#x73;&#x20;&#x61;&#x74;&#x20;&#x72;&#x6f;&#x73;&#x77;&#x65;&#x6c;&#x6c;&#x70;&#x61;&#x72;&#x6b;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("BiocBaseUtils") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("BiocBaseUtils") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("BiocBaseUtils") BiocBaseUtils Quick Start HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License Artistic-2.0 Depends R (>= 4.2.0) Imports methods, utils System Requirements URL Bug Reports https://www.github.com/Bioconductor/BiocBaseUtils/issues See More Suggests knitr, rmarkdown, BiocStyle , tinytest Linking To Enhances Depends On Me Imports Me BiocFHIR , DNAfusion , MultiAssayExperiment , TENxIO , UniProt.ws Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package BiocBaseUtils_1.0.0.tar.gz Windows Binary BiocBaseUtils_1.0.0.zip macOS Binary (x86_64) BiocBaseUtils_1.0.0.tgz macOS Binary (arm64) BiocBaseUtils_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/BiocBaseUtils Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiocBaseUtils Bioc Package Browser https://code.bioconductor.org/browse/BiocBaseUtils/ Package Short Url https://bioconductor.org/packages/BiocBaseUtils/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-biocbaseutils --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-biocbaseutils 1.0.0 r42hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-biocbaseutils-1.0.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-biocbaseutils
+version     : 1.0.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 258 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.0.0-r42hdfd78af_0.tar.bz2
+md5         : 0f3515f24a98b90e00f6b9953e56f070
+timestamp   : 2022-11-03 08:25:37 UTC
+dependencies: 
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-biocbaseutils 1.2.0 r43hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-biocbaseutils-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-biocbaseutils
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 258 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : 63f12ce657dddc1e30f73517b681da6b
+timestamp   : 2023-07-07 10:48:06 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-biocbaseutils 1.4.0 r43hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-biocbaseutils-1.4.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-biocbaseutils
+version     : 1.4.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 259 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.4.0-r43hdfd78af_0.tar.bz2
+md5         : 5c6865ae9bb4f7bb72001e67947d271c
+timestamp   : 2023-12-03 20:52:53 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-biocbaseutils 1.8.0 r44hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-biocbaseutils-1.8.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-biocbaseutils
+version     : 1.8.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 272 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.8.0-r44hdfd78af_0.tar.bz2
+md5         : 8989603129d36f81b85d0665e3b29708
+timestamp   : 2024-12-14 18:05:38 UTC
+dependencies: 
+  - r-base >=4.4,<4.5.0a0
+
+
+bioconductor-biocbaseutils 1.12.0 r45hdfd78af_0
+-----------------------------------------------
+file name   : bioconductor-biocbaseutils-1.12.0-r45hdfd78af_0.conda
+name        : bioconductor-biocbaseutils
+version     : 1.12.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 244 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-biocbaseutils-1.12.0-r45hdfd78af_0.conda
+md5         : 2c13015debedd6c56e5d789ef7ca4db3
+timestamp   : 2026-02-06 22:20:04 UTC
+dependencies: 
+  - r-base >=4.5,<4.6.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biomformat.manual_bundle.txt

@@ -0,0 +1,433 @@
+# Tool: bioconductor-biomformat
+software_name: bioconductor-biomformat
+tier: T1
+domain: t1_backfill_overall
+downloads: 261080
+summary: An interface package for the BIOM file format
+description: This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
+dependencies: bioconductor-rhdf5 >=2.54.0,<2.55.0, r-base >=4.5,<4.6.0a0, r-jsonlite >=0.9.16, r-matrix >=1.2, r-plyr >=1.8
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/biomformat.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/biomformat.html
+Bioconductor - biomformat Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages biomformat biomformat This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see biomformat . An interface package for the BIOM file format DOI: 10.18129/B9.bioc.biomformat Bioconductor version: 3.22 This is an R package for interfacing with the BIOM file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods. Author: Paul J. McMurdie [aut, cre], Joseph N. Paulson [aut] Maintainer: Paul J. McMurdie &#x3c;&#x6a;&#x6f;&#x65;&#x79;&#x37;&#x31;&#x31;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("biomformat") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biomformat") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("biomformat") The biomformat package Vignette HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , ImmunoOncology , Metagenomics , Microbiome , Software Version 1.38.3 In Bioconductor since BioC 3.3 (R-3.3) (10 years) License GPL-2 Depends R (>= 4.1), methods Imports jsonlite (>= 0.9.16), Matrix (>= 1.7-0) System Requirements URL https://github.com/joey711/biomformat/ http://biom-format.org/ Bug Reports https://github.com/joey711/biomformat/issues See More Suggests testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7), rhdf5 Linking To Enhances Depends On Me Imports Me microbiomeExplorer , phyloseq Suggests Me animalcules , iSEEtree , metagenomeSeq , MGnifyR , mia , MicrobiotaProcess , MetaScope Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package biomformat_1.38.3.tar.gz Windows Binary (x86_64) biomformat_1.38.3.zip macOS Binary (x86_64) biomformat_1.38.3.tgz macOS Binary (arm64) biomformat_1.38.3.tgz Source Repository git clone https://git.bioconductor.org/packages/biomformat Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biomformat Bioc Package Browser https://code.bioconductor.org/browse/biomformat/ Package Short Url https://bioconductor.org/packages/biomformat/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-biomformat --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-biomformat 1.0.2 0
+-------------------------------
+file name   : bioconductor-biomformat-1.0.2-0.tar.bz2
+name        : bioconductor-biomformat
+version     : 1.0.2
+build       : 0
+build number: 0
+size        : 175 KB
+license     : AGPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.0.2-0.tar.bz2
+md5         : d1a2d06babb85c8e83d071325d590ba3
+dependencies: 
+  - bioconductor-biobase
+  - bioconductor-rhdf5 >=2.16.0
+  - r >=3.2.0
+  - r-jsonlite >=0.9.16
+  - r-matrix >=1.2
+  - r-plyr >=1.8
+
+
+bioconductor-biomformat 1.0.2 r3.3.1_1
+--------------------------------------
+file name   : bioconductor-biomformat-1.0.2-r3.3.1_1.tar.bz2
+name        : bioconductor-biomformat
+version     : 1.0.2
+build       : r3.3.1_1
+build number: 1
+size        : 176 KB
+license     : GPL-2
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biomformat-1.0.2-r3.3.1_1.tar.bz2
+md5         : 53fdd76b030c40d07dbd652bbae01302
+dependencies: 
+  - bioconductor-rhdf5
+  - r 3.3.1*
+  - r-jsonlite >=0.9.16
+  - r-plyr >=1.8
+
+
+bioconductor-biomformat 1.2.0 r3.3.1_0
+--------------------------------------
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+--------------------------------------
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+--------------------------------------
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+--------------------------------------
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+--------------------------------------
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+file name   : bioconductor-biomformat-1.26.0-r42hdfd78af_0.tar.bz2
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BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-biovizbase.manual_bundle.txt

@@ -0,0 +1,378 @@
+# Tool: bioconductor-biovizbase
+software_name: bioconductor-biovizbase
+tier: T1
+domain: t1_backfill_overall
+downloads: 129312
+summary: Basic graphic utilities for visualization of genomic data.
+description: The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.
+dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-annotationdbi >=1.72.0,<1.73.0a0, bioconductor-annotationfilter >=1.34.0,<1.35.0, bioconductor-annotationfilter >=1.34.0,<1.35.0a0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-biostrings >=2.78.0,<2.79.0, bioconductor-biostrings >=2.78.0,<2.79.0a0, bioconductor-ensembldb >=2.34.0,<2.35.0, bioconductor-ensembldb >=2.34.0,<2.35.0a0, bioconductor-genomeinfodb >=1.46.0,<1.47.0, bioconductor-genomeinfodb >=1.46.2,<1.47.0a0, bioconductor-genomicalignments >=1.46.0,<1.47.0, bioconductor-genomicalignments >=1.46.0,<1.47.0a0, bioconductor-genomicfeatures >=1.62.0,<1.63.0, bioconductor-genomicfeatures >=1.62.0,<1.63.0a0, bioconductor-genomicranges >=1.62.0,<1.63.0, bioconductor-genomicranges >=1.62.1,<1.63.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-rsamtools >=2.26.0,<2.27.0, bioconductor-rsamtools >=2.26.0,<2.27.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-seqinfo >=1.0.0,<1.1.0, bioconductor-seqinfo >=1.0.0,<1.1.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, bioconductor-variantannotation >=1.56.0,<1.57.0, bioconductor-variantannotation >=1.56.0,<1.57.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-dichromat, r-hmisc, r-rcolorbrewer, r-rlang, r-scales
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/biovizBase.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/biovizBase.html
+Bioconductor - biovizBase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages biovizBase biovizBase This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see biovizBase . Basic graphic utilities for visualization of genomic data. DOI: 10.18129/B9.bioc.biovizBase Bioconductor version: 3.22 The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency. Author: Tengfei Yin [aut], Michael Lawrence [aut, ths, cre], Dianne Cook [aut, ths], Johannes Rainer [ctb] Maintainer: Michael Lawrence &#x3c;&#x6c;&#x61;&#x77;&#x72;&#x65;&#x6d;&#x69;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("biovizBase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("biovizBase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("biovizBase") An Introduction to biovizBase PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Preprocessing , Software , Visualization Version 1.58.0 In Bioconductor since BioC 2.9 (R-2.14) (14.5 years) License Artistic-2.0 Depends R (>= 3.5.0), methods Imports grDevices, stats, scales , Hmisc , RColorBrewer , dichromat , BiocGenerics , S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), Seqinfo , GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), GenomicFeatures (>= 1.61.4), AnnotationDbi , VariantAnnotation (>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>= 0.99.8), rlang System Requirements URL See More Suggests BSgenome.Hsapiens.UCSC.hg19 , TxDb.Hsapiens.UCSC.hg19.knownGene , BSgenome , rtracklayer , EnsDb.Hsapiens.v75 , RUnit Linking To Enhances Depends On Me CAFE Imports Me ChIPexoQual , ggbio , Gviz , karyoploteR , Pviz , Rqc Suggests Me Damsel , derfinderPlot , FRASER , NanoStringNCTools , OUTRIDER , R3CPET , regionReport , StructuralVariantAnnotation , Signac Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package biovizBase_1.58.0.tar.gz Windows Binary (x86_64) biovizBase_1.58.0.zip macOS Binary (x86_64) biovizBase_1.58.0.tgz macOS Binary (arm64) biovizBase_1.58.0.tgz Source Repository git clone https://git.bioconductor.org/packages/biovizBase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/biovizBase Bioc Package Browser https://code.bioconductor.org/browse/biovizBase/ Package Short Url https://bioconductor.org/packages/biovizBase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-biovizbase --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-biovizbase 1.18.0 0
+--------------------------------
+file name   : bioconductor-biovizbase-1.18.0-0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.18.0
+build       : 0
+build number: 0
+size        : 2.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.18.0-0.tar.bz2
+md5         : 1436bfdf77c830117ac80003c318f02e
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.17.19
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.2.4
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r >=2.10
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.18.0 1
+--------------------------------
+file name   : bioconductor-biovizbase-1.18.0-1.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.18.0
+build       : 1
+build number: 1
+size        : 2.2 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.18.0-1.tar.bz2
+md5         : c9b2b753cadc591df93754b8758aea8d
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.17.19
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.2.4
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r >=2.10
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.20.0 r3.3.1_0
+---------------------------------------
+file name   : bioconductor-biovizbase-1.20.0-r3.3.1_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.20.0
+build       : r3.3.1_0
+build number: 0
+size        : 2.2 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.3.1_0.tar.bz2
+md5         : 98a9649cf285d7bee64b887978b35a5d
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-ensembldb >=1.3.8
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.23.21
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.9.25
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r 3.3.1*
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.20.0 r3.3.2_0
+---------------------------------------
+file name   : bioconductor-biovizbase-1.20.0-r3.3.2_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.20.0
+build       : r3.3.2_0
+build number: 0
+size        : 2.2 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.3.2_0.tar.bz2
+md5         : 197db4210f0e0be35f8d86f321f108f6
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-ensembldb >=1.3.8
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.23.21
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.9.25
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r-base 3.3.2*
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.20.0 r3.4.1_0
+---------------------------------------
+file name   : bioconductor-biovizbase-1.20.0-r3.4.1_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.20.0
+build       : r3.4.1_0
+build number: 0
+size        : 2.2 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.20.0-r3.4.1_0.tar.bz2
+md5         : 299879d4f375a97b75cd78dbd295677c
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-ensembldb >=1.3.8
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.23.21
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.9.25
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r-base 3.4.1*
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.24.0 r3.4.1_0
+---------------------------------------
+file name   : bioconductor-biovizbase-1.24.0-r3.4.1_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.24.0
+build       : r3.4.1_0
+build number: 0
+size        : 2.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.24.0-r3.4.1_0.tar.bz2
+md5         : 49b504c027b56a4d70d7d3f3d374225a
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-annotationfilter >=0.99.8
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-ensembldb >=1.99.13
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.23.21
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.9.25
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r-base 3.4.1*
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.26.0 r3.4.1_0
+---------------------------------------
+file name   : bioconductor-biovizbase-1.26.0-r3.4.1_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.26.0
+build       : r3.4.1_0
+build number: 0
+size        : 2.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.26.0-r3.4.1_0.tar.bz2
+md5         : 1d795cb7f1ac8e6ebcec1ede2dcd0e49
+dependencies: 
+  - bioconductor-annotationdbi
+  - bioconductor-annotationfilter >=0.99.8
+  - bioconductor-biocgenerics
+  - bioconductor-biostrings >=2.33.11
+  - bioconductor-ensembldb >=1.99.13
+  - bioconductor-genomeinfodb >=1.5.14
+  - bioconductor-genomicalignments >=1.1.16
+  - bioconductor-genomicfeatures >=1.21.19
+  - bioconductor-genomicranges >=1.23.21
+  - bioconductor-iranges >=1.99.28
+  - bioconductor-rsamtools >=1.17.28
+  - bioconductor-s4vectors >=0.9.25
+  - bioconductor-summarizedexperiment
+  - bioconductor-variantannotation >=1.11.4
+  - r-base 3.4.1*
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-scales
+
+
+bioconductor-biovizbase 1.28.2 r341h470a237_0
+---------------------------------------------
+file name   : bioconductor-biovizbase-1.28.2-r341h470a237_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.28.2
+build       : r341h470a237_0
+build number: 0
+size        : 2.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.28.2-r341h470a237_0.tar.bz2
+md5         : 47bbe53778002ca0e9d01f0802846b85
+timestamp   : 2018-10-22 19:38:10 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - bioconductor-annotationfilter >=1.4.0,<1.6.0
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - bioconductor-biostrings >=2.48.0,<2.50.0
+  - bioconductor-ensembldb >=2.4.1,<2.6.0
+  - bioconductor-genomeinfodb >=1.16.0,<1.18.0
+  - bioconductor-genomicalignments >=1.16.0,<1.18.0
+  - bioconductor-genomicfeatures >=1.32.2,<1.34.0
+  - bioconductor-genomicranges >=1.32.7,<1.34.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-rsamtools >=1.32.3,<1.34.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - bioconductor-summarizedexperiment >=1.10.1,<1.12.0
+  - bioconductor-variantannotation >=1.26.1,<1.28.0
+  - libgcc-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-rlang
+  - r-scales
+
+
+bioconductor-biovizbase 1.28.2 r351h470a237_0
+---------------------------------------------
+file name   : bioconductor-biovizbase-1.28.2-r351h470a237_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.28.2
+build       : r351h470a237_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.28.2-r351h470a237_0.tar.bz2
+md5         : 9ee3304b280c3f7946ee1ca929e855a7
+timestamp   : 2018-10-22 19:41:41 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - bioconductor-annotationfilter >=1.4.0,<1.6.0
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - bioconductor-biostrings >=2.48.0,<2.50.0
+  - bioconductor-ensembldb >=2.4.1,<2.6.0
+  - bioconductor-genomeinfodb >=1.16.0,<1.18.0
+  - bioconductor-genomicalignments >=1.16.0,<1.18.0
+  - bioconductor-genomicfeatures >=1.32.2,<1.34.0
+  - bioconductor-genomicranges >=1.32.7,<1.34.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-rsamtools >=1.32.3,<1.34.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - bioconductor-summarizedexperiment >=1.10.1,<1.12.0
+  - bioconductor-variantannotation >=1.26.1,<1.28.0
+  - libgcc-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-rlang
+  - r-scales
+
+
+bioconductor-biovizbase 1.30.1 r351h14c3975_0
+---------------------------------------------
+file name   : bioconductor-biovizbase-1.30.1-r351h14c3975_0.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.30.1
+build       : r351h14c3975_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.30.1-r351h14c3975_0.tar.bz2
+md5         : 540932ffd64a66b7d15ab27e0a9bc032
+timestamp   : 2018-12-30 07:59:24 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.44.0,<1.45.0
+  - bioconductor-annotationfilter >=1.6.0,<1.7.0
+  - bioconductor-biocgenerics >=0.28.0,<0.29.0
+  - bioconductor-biostrings >=2.50.0,<2.51.0
+  - bioconductor-ensembldb >=2.6.0,<2.7.0
+  - bioconductor-genomeinfodb >=1.18.0,<1.19.0
+  - bioconductor-genomicalignments >=1.18.0,<1.19.0
+  - bioconductor-genomicfeatures >=1.34.0,<1.35.0
+  - bioconductor-genomicranges >=1.34.0,<1.35.0
+  - bioconductor-iranges >=2.16.0,<2.17.0
+  - bioconductor-rsamtools >=1.34.0,<1.35.0
+  - bioconductor-s4vectors >=0.20.0,<0.21.0
+  - bioconductor-summarizedexperiment >=1.12.0,<1.13.0
+  - bioconductor-variantannotation >=1.28.0,<1.29.0
+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-dichromat
+  - r-hmisc
+  - r-rcolorbrewer
+  - r-rlang
+  - r-scales
+
+
+bioconductor-biovizbase 1.32.0 r36h516909a_1
+--------------------------------------------
+file name   : bioconductor-biovizbase-1.32.0-r36h516909a_1.tar.bz2
+name        : bioconductor-biovizbase
+version     : 1.32.0
+build       : r36h516909a_1
+build number: 1
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-biovizbase-1.32.0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-blase.manual_bundle.txt

@@ -0,0 +1,54 @@
+# Tool: bioconductor-blase
+software_name: bioconductor-blase
+tier: T1
+domain: single_cell
+downloads: 35
+summary: Bulk Linking Analysis for Single-cell Experiments
+description: BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-boot, r-dplyr, r-ggplot2, r-matrix, r-mgcv, r-patchwork, r-rlang, r-seurat >=4.0.0, r-viridis
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/blase.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/blase.html
+Bioconductor - blase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages blase blase This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see blase . Bulk Linking Analysis for Single-cell Experiments DOI: 10.18129/B9.bioc.blase Bioconductor version: 3.22 BLASE is a method for finding where bulk RNA-seq data lies on a single-cell pseudotime trajectory. It uses a fast and understandable approach based on Spearman correlation, with bootstrapping to provide confidence. BLASE can be used to "date" bulk RNA-seq data, annotate cell types in scRNA-seq, and help correct for developmental phenotype differences in bulk RNA-seq experiments. Author: Andrew McCluskey [aut, cre] ORCID: 0009-0004-4187-799X , Toby Kettlewell [aut] ORCID: 0009-0001-1225-3318 , Adrian M. Smith [aut] ORCID: 0000-0001-8833-2330 , Rhiannon Kundu [aut] ORCID: 0000-0003-3970-5860 , David A. Gunn [aut] ORCID: 0000-0001-9866-3221 , Thomas D. Otto [aut, ths] ORCID: 0000-0002-1246-7404 Maintainer: Andrew McCluskey &#x3c;&#x32;&#x31;&#x31;&#x37;&#x35;&#x33;&#x32;&#x6d;&#x20;&#x61;&#x74;&#x20;&#x73;&#x74;&#x75;&#x64;&#x65;&#x6e;&#x74;&#x2e;&#x67;&#x6c;&#x61;&#x2e;&#x61;&#x63;&#x2e;&#x75;&#x6b;&#x3e; Citation (from within R, enter citation("blase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("blase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("blase") Assigning bulk RNA-seq to pseudotime HTML R Script BLASE for annotating scRNA-seq HTML R Script BLASE for excluding developmental genes from bulk RNA-seq HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews CellBasedAssays , CellBiology , GeneExpression , RNASeq , Sequencing , SingleCell , Software , TimeCourse , Transcription , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.22 (R-4.5) ( License GPL (>= 3) Depends R (>= 4.5.0) Imports SummarizedExperiment , SingleCellExperiment , ggplot2 , viridis , patchwork , Matrix , scater , methods, rlang , BiocParallel , boot , dplyr , mgcv , stats, MatrixGenerics , Seurat (>= 4.0.0) System Requirements URL https://andrewmccluskey-uog.github.io/blase/ Bug Reports https://andrewmccluskey-uog.github.io/blase/issues See More Suggests knitr , rmarkdown , testthat (>= 3.2.3), covr , tradeSeq , scran , slingshot , tools, ami , reshape2 , plyr , fs , sparseMatrixStats , ggVennDiagram , uwot , BiocStyle , DelayedMatrixStats , limma Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package blase_1.0.0.tar.gz Windows Binary (x86_64) blase_1.0.0.zip (64-bit only) macOS Binary (x86_64) blase_1.0.0.tgz macOS Binary (arm64) blase_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/blase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/blase Bioc Package Browser https://code.bioconductor.org/browse/blase/ Package Short Url https://bioconductor.org/packages/blase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-blase --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-blase 1.0.0 r45hdfd78af_0
+--------------------------------------
+file name   : bioconductor-blase-1.0.0-r45hdfd78af_0.conda
+name        : bioconductor-blase
+version     : 1.0.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 8.1 MB
+license     : GPL (>= 3)
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-blase-1.0.0-r45hdfd78af_0.conda
+md5         : fe1e968e1f0a6996348cc9852006e251
+timestamp   : 2026-03-02 19:14:51 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-matrixgenerics >=1.22.0,<1.23.0
+  - bioconductor-scater >=1.38.0,<1.39.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-base >=4.5,<4.6.0a0
+  - r-boot
+  - r-dplyr
+  - r-ggplot2
+  - r-matrix
+  - r-mgcv
+  - r-patchwork
+  - r-rlang
+  - r-seurat >=4.0.0
+  - r-viridis

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-bluster.manual_bundle.txt

@@ -0,0 +1,400 @@
+# Tool: bioconductor-bluster
+software_name: bioconductor-bluster
+tier: T1
+domain: t1_backfill_overall
+downloads: 298329
+summary: Clustering Algorithms for Bioconductor
+description: Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.
+dependencies: bioconductor-assorthead >=1.4.0,<1.5.0, bioconductor-assorthead >=1.4.0,<1.5.0a0, bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-biocneighbors >=2.4.0,<2.5.0a0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-cluster, r-igraph, r-matrix, r-rcpp
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.12/bioc/html/bluster.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.12/bioc/html/bluster.html
+Bioconductor - bluster About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.12 Software Packages bluster bluster This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see bluster . Clustering Algorithms for Bioconductor DOI: 10.18129/B9.bioc.bluster Bioconductor version: 3.12 Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results. Author: Aaron Lun [aut, cre] Maintainer: Aaron Lun &#x3c;&#x69;&#x6e;&#x66;&#x69;&#x6e;&#x69;&#x74;&#x65;&#x2e;&#x6d;&#x6f;&#x6e;&#x6b;&#x65;&#x79;&#x73;&#x2e;&#x77;&#x69;&#x74;&#x68;&#x2e;&#x6b;&#x65;&#x79;&#x62;&#x6f;&#x61;&#x72;&#x64;&#x73;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("bluster") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("bluster") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("bluster") 1. Clustering algorithms HTML R Script 2. Clustering diagnostics HTML R Script Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , GeneExpression , ImmunoOncology , SingleCell , Software , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.12 (R-4.0) (3.5 years) License GPL-3 Depends Imports stats, methods, utils, Matrix, Rcpp, igraph, S4Vectors , BiocParallel , BiocNeighbors System Requirements C++11 URL See More Suggests knitr, rmarkdown, testthat, BiocStyle , dynamicTreeCut, scRNAseq , scuttle , scater , scran , pheatmap, viridis Linking To Rcpp Enhances Depends On Me Imports Me mbkmeans , scDblFinder , scran Suggests Me batchelor , scDblFinder Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package bluster_1.0.0.tar.gz Windows Binary bluster_1.0.0.zip (32- &amp; 64-bit) macOS 10.13 (High Sierra) bluster_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/bluster Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bluster Bioc Package Browser https://code.bioconductor.org/browse/bluster/ Package Short Url https://bioconductor.org/packages/bluster/ Package Downloads Report Download Stats Old Source Packages for BioC 3.12 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-bluster --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-bluster 1.0.0 r40h399db7b_2
+----------------------------------------
+file name   : bioconductor-bluster-1.0.0-r40h399db7b_2.tar.bz2
+name        : bioconductor-bluster
+version     : 1.0.0
+build       : r40h399db7b_2
+build number: 2
+size        : 1.9 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.0.0-r40h399db7b_2.tar.bz2
+md5         : 3abe66fe95f469660bec08863c25ebee
+timestamp   : 2021-03-28 09:23:33 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.8.0,<1.9.0
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.0.0 r40h5f743cb_1
+----------------------------------------
+file name   : bioconductor-bluster-1.0.0-r40h5f743cb_1.tar.bz2
+name        : bioconductor-bluster
+version     : 1.0.0
+build       : r40h5f743cb_1
+build number: 1
+size        : 1.9 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.0.0-r40h5f743cb_1.tar.bz2
+md5         : 3ac47a83a2a46b72b786ed9c70ac2b9b
+timestamp   : 2020-10-29 22:55:55 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.8.0,<1.9.0
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=7.5.0
+  - r-base >=4.0,<4.1.0a0
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.2.1 r41h399db7b_0
+----------------------------------------
+file name   : bioconductor-bluster-1.2.1-r41h399db7b_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.2.1
+build       : r41h399db7b_0
+build number: 0
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.2.1-r41h399db7b_0.tar.bz2
+md5         : 31696c11752a86009b5d0b2868577329
+timestamp   : 2021-05-31 20:11:19 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.10.0,<1.11.0
+  - bioconductor-biocparallel >=1.26.0,<1.27.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.4.0 r41h399db7b_0
+----------------------------------------
+file name   : bioconductor-bluster-1.4.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.4.0
+build       : r41h399db7b_0
+build number: 0
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41h399db7b_0.tar.bz2
+md5         : 8155293d00219d8d8572742e506946e1
+timestamp   : 2021-11-02 23:00:34 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.12.0,<1.13.0
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.4.0
+  - r-base >=4.1,<4.2.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.4.0 r41h619a076_1
+----------------------------------------
+file name   : bioconductor-bluster-1.4.0-r41h619a076_1.tar.bz2
+name        : bioconductor-bluster
+version     : 1.4.0
+build       : r41h619a076_1
+build number: 1
+size        : 3.3 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41h619a076_1.tar.bz2
+md5         : 16f1d84bb456be627b38484ac6e7d0ed
+timestamp   : 2022-02-25 08:13:14 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.12.0,<1.13.0
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=10.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.4.0 r41hc247a5b_2
+----------------------------------------
+file name   : bioconductor-bluster-1.4.0-r41hc247a5b_2.tar.bz2
+name        : bioconductor-bluster
+version     : 1.4.0
+build       : r41hc247a5b_2
+build number: 2
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.4.0-r41hc247a5b_2.tar.bz2
+md5         : 64f5ca34acf6c257bbc8de95059068ce
+timestamp   : 2022-09-16 07:23:39 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.12.0,<1.13.0
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.1,<4.2.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.8.0 r42hc247a5b_0
+----------------------------------------
+file name   : bioconductor-bluster-1.8.0-r42hc247a5b_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.8.0
+build       : r42hc247a5b_0
+build number: 0
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.8.0-r42hc247a5b_0.tar.bz2
+md5         : cf5532c02ec232d0212cdc63c349f66d
+timestamp   : 2022-11-04 01:06:55 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.16.0,<1.17.0
+  - bioconductor-biocparallel >=1.32.0,<1.33.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.2,<4.3.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.8.0 r42hf17093f_1
+----------------------------------------
+file name   : bioconductor-bluster-1.8.0-r42hf17093f_1.tar.bz2
+name        : bioconductor-bluster
+version     : 1.8.0
+build       : r42hf17093f_1
+build number: 1
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.8.0-r42hf17093f_1.tar.bz2
+md5         : 233f4186c52aa76d060b6f417db10fa8
+timestamp   : 2023-05-18 19:59:08 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.16.0,<1.17.0
+  - bioconductor-biocparallel >=1.32.0,<1.33.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.2,<4.3.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.10.0 r43hf17093f_0
+-----------------------------------------
+file name   : bioconductor-bluster-1.10.0-r43hf17093f_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.10.0
+build       : r43hf17093f_0
+build number: 0
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.10.0-r43hf17093f_0.tar.bz2
+md5         : 686a5047c656de7c05eb52c62c211500
+timestamp   : 2023-07-10 20:28:55 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.18.0,<1.19.0
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.12.0 r43hf17093f_0
+-----------------------------------------
+file name   : bioconductor-bluster-1.12.0-r43hf17093f_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.12.0
+build       : r43hf17093f_0
+build number: 0
+size        : 3.4 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.12.0-r43hf17093f_0.tar.bz2
+md5         : 4d9175962ce9281e9c7cf325e68a1318
+timestamp   : 2023-12-06 05:15:25 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.20.0,<1.21.0
+  - bioconductor-biocneighbors >=1.20.0,<1.21.0a0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0a0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-s4vectors >=0.40.2,<0.41.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.12.0 r43hf17093f_1
+-----------------------------------------
+file name   : bioconductor-bluster-1.12.0-r43hf17093f_1.tar.bz2
+name        : bioconductor-bluster
+version     : 1.12.0
+build       : r43hf17093f_1
+build number: 1
+size        : 3.4 MB
+license     : GPL-3.0-only
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.12.0-r43hf17093f_1.tar.bz2
+md5         : a161b697cbb86b10f01958034eaa150a
+timestamp   : 2024-05-09 08:53:41 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.20.0,<1.21.0
+  - bioconductor-biocneighbors >=1.20.0,<1.21.0a0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0a0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-s4vectors >=0.40.2,<0.41.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.16.0 r44he5774e6_0
+-----------------------------------------
+file name   : bioconductor-bluster-1.16.0-r44he5774e6_0.tar.bz2
+name        : bioconductor-bluster
+version     : 1.16.0
+build       : r44he5774e6_0
+build number: 0
+size        : 3.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.16.0-r44he5774e6_0.tar.bz2
+md5         : 5d6d1603364e2b6b5c9ce378ba01c054
+timestamp   : 2024-12-16 19:52:58 UTC
+dependencies: 
+  - bioconductor-assorthead >=1.0.0,<1.1.0
+  - bioconductor-assorthead >=1.0.0,<1.1.0a0
+  - bioconductor-biocneighbors >=2.0.0,<2.1.0
+  - bioconductor-biocneighbors >=2.0.0,<2.1.0a0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0a0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx >=13
+  - r-base >=4.4,<4.5.0a0
+  - r-cluster
+  - r-igraph
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-bluster 1.16.0 r44he5774e6_1
+-----------------------------------------
+file name   : bioconductor-bluster-1.16.0-r44he5774e6_1.tar.bz2
+name        : bioconductor-bluster
+version     : 1.16.0
+build       : r44he5774e6_1
+build number: 1
+size        : 3.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-bluster-1.16.0-r44he5774e6_1.tar.bz2
+md5         : ddaf32568fb903b4f2492059baf3a283
+timestamp   : 2025-04-21 22:17:43 UTC
+dependencies: 
+  - bioconductor-assorthead >=1.0.0,<1.1.0
+  - bioconductor-assorthead >=1.0.0,<1.1.0a0
+  - bioconductor-biocneighbors >=2.0.0,<2.1.0
+  - bioconductor-biocneighbors >=2.0.0,<2.1.0a0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0a0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx >=13
+  - r-base >=4.4,<4.5.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cardspa.manual_bundle.txt

@@ -0,0 +1,79 @@
+# Tool: bioconductor-cardspa
+software_name: bioconductor-cardspa
+tier: T1
+domain: spatial_transcriptomics
+downloads: 276
+summary: Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics
+description: CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-concaveman, r-dplyr, r-fields, r-ggcorrplot, r-ggplot2, r-gtools, r-matrix, r-mcmcpack, r-nmf, r-nnls, r-rann, r-rcolorbrewer, r-rcpp >=1.0.7, r-rcpparmadillo, r-reshape2, r-scatterpie, r-sf, r-sp, r-spatstat.random, r-wrmisc
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/CARDspa.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/CARDspa.html
+Bioconductor - CARDspa Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages CARDspa CARDspa This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see CARDspa . Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics DOI: 10.18129/B9.bioc.CARDspa Bioconductor version: 3.22 CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes. Author: Ying Ma [aut], Jing Fu [cre] Maintainer: Jing Fu &#x3c;&#x6a;&#x69;&#x6e;&#x67;&#x5f;&#x66;&#x75;&#x20;&#x61;&#x74;&#x20;&#x62;&#x72;&#x6f;&#x77;&#x6e;&#x2e;&#x65;&#x64;&#x75;&#x3e; Citation (from within R, enter citation("CARDspa") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CARDspa") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CARDspa") Example_Analysis HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews SingleCell , Software , Spatial , Transcriptomics , Visualization Version 1.2.1 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License GPL-3 + file LICENSE Depends R (>= 4.3.0) Imports Rcpp (>= 1.0.7), RcppArmadillo , SummarizedExperiment , methods, MCMCpack , fields , wrMisc , concaveman , sp , dplyr , sf , Matrix , RANN , ggplot2 , reshape2 , RColorBrewer , S4Vectors , scatterpie , grDevices, ggcorrplot , stats, nnls , BiocParallel , NMF , spatstat.random , gtools , SingleCellExperiment , SpatialExperiment System Requirements URL https://github.com/YMa-lab/CARDspa Bug Reports https://github.com/YMa-lab/CARDspa/issues See More Suggests knitr , rmarkdown , testthat , RcppML , BiocStyle Linking To Rcpp , RcppArmadillo Enhances Depends On Me Imports Me OSTA Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CARDspa_1.2.1.tar.gz Windows Binary (x86_64) CARDspa_1.2.1.zip macOS Binary (x86_64) CARDspa_1.2.1.tgz macOS Binary (arm64) CARDspa_1.2.1.tgz Source Repository git clone https://git.bioconductor.org/packages/CARDspa Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CARDspa Bioc Package Browser https://code.bioconductor.org/browse/CARDspa/ Package Short Url https://bioconductor.org/packages/CARDspa/ Package Downloads Report Download Stats Old Source Packages for BioC 3.22 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-cardspa --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-cardspa 1.2.1 r45ha27e39d_0
+----------------------------------------
+file name   : bioconductor-cardspa-1.2.1-r45ha27e39d_0.conda
+name        : bioconductor-cardspa
+version     : 1.2.1
+build       : r45ha27e39d_0
+build number: 0
+size        : 4.2 MB
+license     : GPL-3 + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-cardspa-1.2.1-r45ha27e39d_0.conda
+md5         : 324a1f797d951efb351a04728f598cb6
+timestamp   : 2026-03-15 00:19:20 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-biocparallel >=1.44.0,<1.45.0a0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0a0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0a0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=14
+  - liblapack >=3.9.0,<4.0a0
+  - liblzma >=5.8.2,<6.0a0
+  - libstdcxx >=14
+  - libzlib >=1.3.1,<2.0a0
+  - r-base >=4.5,<4.6.0a0
+  - r-concaveman
+  - r-dplyr
+  - r-fields
+  - r-ggcorrplot
+  - r-ggplot2
+  - r-gtools
+  - r-matrix
+  - r-mcmcpack
+  - r-nmf
+  - r-nnls
+  - r-rann
+  - r-rcolorbrewer
+  - r-rcpp >=1.0.7
+  - r-rcpparmadillo
+  - r-reshape2
+  - r-scatterpie
+  - r-sf
+  - r-sp
+  - r-spatstat.random
+  - r-wrmisc

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-catscradle.manual_bundle.txt

@@ -0,0 +1,99 @@
+# Tool: bioconductor-catscradle
+software_name: bioconductor-catscradle
+tier: T1
+domain: single_cell
+downloads: 564
+summary: This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters
+description: This package addresses two broad areas.  It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods.  These are contiguous regions of tissue surrounding individual cells.  'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them.  In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells.  In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.
+dependencies: bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-abind, r-base >=4.5,<4.6.0a0, r-data.table, r-geometry, r-ggplot2, r-igraph, r-matrix, r-msigdbr, r-networkd3, r-pheatmap, r-pracma, r-rdist, r-reshape2, r-rfast, r-seurat >=5.0.1, r-seuratobject, r-stringr
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.20/bioc/html/CatsCradle.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.20/bioc/html/CatsCradle.html
+Bioconductor - CatsCradle Registration and Abstract Submission Open for GBCC2025 : Joint Galaxy/Bioconductor Conference Early registration discount pricing ends March 31! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.20 Software Packages CatsCradle CatsCradle This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see CatsCradle . This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters DOI: 10.18129/B9.bioc.CatsCradle Bioconductor version: 3.20 This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes. Author: Anna Laddach [aut] ORCID: 0000-0001-5552-6534 , Michael Shapiro [aut, cre] ORCID: 0000-0002-2769-9320 Maintainer: Michael Shapiro &#x3c;&#x6d;&#x69;&#x63;&#x68;&#x61;&#x65;&#x6c;&#x2e;&#x73;&#x68;&#x61;&#x70;&#x69;&#x72;&#x6f;&#x20;&#x61;&#x74;&#x20;&#x63;&#x72;&#x69;&#x63;&#x6b;&#x2e;&#x61;&#x63;&#x2e;&#x75;&#x6b;&#x3e; Citation (from within R, enter citation("CatsCradle") ): Installation To install this package, start R (version "4.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CatsCradle") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CatsCradle") CatsCradle HTML R Script CatsCradle Example Data HTML R Script CatsCradle Quick Start HTML R Script CatsCradle SingleCellExperiment Quick Start HTML R Script CatsCradle Spatial Vignette HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews BiologicalQuestion , GeneExpression , SingleCell , Software , Spatial , StatisticalMethod , Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.20 (R-4.4) ( License MIT + file LICENSE Depends R (>= 4.4.0) Imports Seurat (>= 5.0.1), ggplot2 , networkD3 , stringr , pracma , reshape2 , rdist , igraph , geometry , Rfast , data.table , abind , pheatmap , EBImage , S4Vectors , SeuratObject , SingleCellExperiment , SpatialExperiment , Matrix , methods, SummarizedExperiment , msigdbr System Requirements URL https://github.com/AnnaLaddach/CatsCradle Bug Reports https://github.com/AnnaLaddach/CatsCradle/issues See More Suggests fossil , interp , knitr , BiocStyle , tictoc Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CatsCradle_1.0.1.tar.gz Windows Binary (x86_64) CatsCradle_1.0.1.zip macOS Binary (x86_64) CatsCradle_1.0.1.tgz macOS Binary (arm64) CatsCradle_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/CatsCradle Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CatsCradle Bioc Package Browser https://code.bioconductor.org/browse/CatsCradle/ Package Short Url https://bioconductor.org/packages/CatsCradle/ Package Downloads Report Download Stats Old Source Packages for BioC 3.20 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2025 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-catscradle --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-catscradle 1.0.0 r44hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-catscradle-1.0.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-catscradle
+version     : 1.0.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 6.0 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-catscradle-1.0.0-r44hdfd78af_0.tar.bz2
+md5         : dc13cebb4b78cb62a91feb1640248dd5
+timestamp   : 2024-12-22 11:02:03 UTC
+dependencies: 
+  - bioconductor-ebimage >=4.48.0,<4.49.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-singlecellexperiment >=1.28.0,<1.29.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - r-abind
+  - r-base >=4.4,<4.5.0a0
+  - r-data.table
+  - r-geometry
+  - r-ggplot2
+  - r-igraph
+  - r-matrix
+  - r-msigdbr
+  - r-networkd3
+  - r-pheatmap
+  - r-pracma
+  - r-rdist
+  - r-reshape2
+  - r-rfast
+  - r-seurat >=5.0.1
+  - r-seuratobject
+  - r-stringr
+
+
+bioconductor-catscradle 1.4.2 r45hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-catscradle-1.4.2-r45hdfd78af_0.conda
+name        : bioconductor-catscradle
+version     : 1.4.2
+build       : r45hdfd78af_0
+build number: 0
+size        : 5.8 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-catscradle-1.4.2-r45hdfd78af_0.conda
+md5         : bf451f7f292d26550bf26901609b2842
+timestamp   : 2026-03-01 20:13:36 UTC
+dependencies: 
+  - bioconductor-ebimage >=4.52.0,<4.53.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-abind
+  - r-base >=4.5,<4.6.0a0
+  - r-data.table
+  - r-geometry
+  - r-ggplot2
+  - r-igraph
+  - r-matrix
+  - r-msigdbr
+  - r-networkd3
+  - r-pheatmap
+  - r-pracma
+  - r-rdist
+  - r-reshape2
+  - r-rfast
+  - r-seurat >=5.0.1
+  - r-seuratobject
+  - r-stringr

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-cellhashr.manual_bundle.txt

@@ -0,0 +1,67 @@
+# Tool: bioconductor-cellhashr
+software_name: bioconductor-cellhashr
+tier: T1
+domain: single_cell
+downloads: 1190
+summary: An R package designed to demultiplex cell hashing data.
+    More information in https://bimberlab.github.io/cellhashR/Lab B (2024). 
+   cellhashR: A Package for Demultiplexing Cell Hashing Data.
+description: An R package designed to demultiplex cell hashing data.
+    More information in https://bimberlab.github.io/cellhashR/Lab B (2024). 
+   cellhashR: A Package for Demultiplexing Cell Hashing Data.
+dependencies: bioconductor-demuxmix, bioconductor-dropletutils, bioconductor-nempi, bioconductor-preprocesscore, r-base >=4.3,<4.4.0a0, r-devtools, r-egg, r-essentials, r-ggextra, r-ggforce, r-ggthemes, r-patchwork, r-rcpp, r-rcpparmadillo, r-rcppeigen, r-rcppparallel, r-rcppprogress, r-reticulate, r-rmdformats, r-seurat, r-seuratobject
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://github.com/BimberLab/cellhashR
+doc_url: 
+dev_url: https://github.com/BimberLab/cellhashR
+
+## URL Docs Extract
+### https://github.com/BimberLab/cellhashR
+GitHub - BimberLab/cellhashR: An R package designed to demultiplex cell hashing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BimberLab / cellhashR Public Notifications You must be signed in to change notification settings Fork 8 Star 31 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights BimberLab/cellhashR master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 224 Commits 224 Commits .github .github R R inst/ rmd inst/ rmd man man tests tests vignettes vignettes .Rbuildignore .Rbuildignore .dockerignore .dockerignore .gitignore .gitignore DESCRIPTION DESCRIPTION Dockerfile Dockerfile NAMESPACE NAMESPACE README.md README.md _pkgdown.yml _pkgdown.yml cellhashR.iml cellhashR.iml View all files Repository files navigation README cellhashR An R package designed to demultiplex cell hashing data. Please see our documentation for more detail . Table of Contents Overview Example Usage Installation Known Issues Development Guidelines Overview Cell hashing is a method that allows sample multiplexing or super-loading within single-cell RNA-seq platforms, such as 10x genomics, originally developed at New York Genome Center in collaboration with the Satija lab. See here for more detail on the technique . The general idea is that cells are labeled with a staining reagent (such as an antibody) tagged with a short nucleotide barcode. Other staining methods have been published, such as the lipid-based Multi-Seq ( https://www.ncbi.nlm.nih.gov/pubmed/31209384 ). In all methods, the hashtag oligo/barcode is sequenced in parallel with cellular mRNA, creating a separate cell hashing library. After sequencing, the cell barcode and hashing index are parsed using tools like Cite-seq-Count ( https://github.com/Hoohm/CITE-seq-Count ), creating a count matrix with the total hash tag counts per cell. Once the count matrix is created, an algorithm must be used to demultiplex cells and assign them to hash tags (i.e. sample). This is where cellhashR comes in. This package provides several functions: Quality control reports for the cell hashing library, covering read counts and normalization. Think FASTQC , except for cell hashing data. A single interface to run one or more demutiplexing algorithms, including the novel demultiplexing algorithms BFF_raw and BFF_cluster. Each algorithm has pros and cons, and will perform better or worse under certain conditions (though in our experience, of the algorithms we have tested, the BFF algorithms work most consistently and under the widest variety of conditions). If you select multiple algorithms (our default workflow), cellhashR will score cells using the consensus call from the set. Various QC summaries are produced during this process as well, if debugging is needed. In addition to the BFF demultiplexing algorithms, other algorithms that can be run from cellhashR include: GMM-Demux demuxEM (see extra requirements below) demuxmix (see extra requirements below) deMULTIplex HTODemux from Seurat hashedDrops from DropletUtils The workflow produces a unified table with the results of each caller and the consensus call. Final QC plots and summaries are created. Each step of the workflow can either be run interactively in R (through the terminal or RStudio), or it can be executed as a pipeline that runs all commands and creates the call table and an HTML report. Click here to view an example QC report Consensus Calling In addition to allowing one to run multiple demuliplexing algorithms to compare results, cellhashR can generate a consensus call based on those scores. This can be useful, since some algorithms will perform better or worse under some conditions. This is automatically built into the dataframe returned by GenerateCellHashingCalls(). Some additional parameters that might be worth considering are: There are separate arguments for 'methods' (i.e. which algorithms will be run), and 'methodsForConsensus', which determined the subset that will be used for the consensus call. majorityConsensusThreshold: This applies to calculating a consensus call when multiple algorithms are used. If NULL, then all non-negative calls must agree or that cell is marked discordant. If non-NULL, then the number of algorithms returning the top call is divided by the total number of non-negative calls. If this ratio is above the majorityConsensusThreshold, that value is selected. For example, when majorityConsensusThreshold=0.6 and the calls are: HTO-1,HTO-1,Negative,HTO-2, then 2/3 calls are for HTO-1, giving 0.66. This is greater than the majorityConsensusThreshold of 0.6, so HTO-1 is returned. This can be useful for situations where most algorithms agree, but a single caller fails. callerDisagreementThreshold: If provided, the agreement rate will be calculated between each caller and the simple majority call, ignoring discordant and no-call cells. If any caller has an disagreement rate above this threshold, it will be dropped and the consensus call re-calculated. The general idea is to drop a caller that is systematically discordant. Example Usage Below are the primary functions of cellhashR needed to QC and score hashing data: # Example 1: parse CITE-seq-Count output, printing QC barcodeData &lt;- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 ) # Example 2: parse CITE-seq-Count output, providing a barcode whitelist. barcodeData &lt;- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' , ' HTO-4 ' , ' HTO-6 ' )) # Create QC plots of barcode normalization PlotNormalizationQC( barcodeData ) # Generate the final cell hashing calls calls &lt;- GenerateCellHashingCalls( barcodeMatrix = barcodeData , methods = c( ' multiseq ' , ' htodemux ' )) # Inspect negative cells: SummarizeCellsByClassification( calls = calls , barcodeMatrix = barcodeData ) Or export/save a template RMarkdown file outlining the default workflow, which can be run interactively or headlessly as part of a pipeline: GetExampleMarkdown( dest = ' cellhashR_template.rmd ' ) Finally, the workflow can be executed using this wrapper around the Rmarkdown, producing a TSV of calls and HTML QC report: CallAndGenerateReport( rawCountData = ' myCountDir/umi_count ' , reportFile = ' report.html ' , callFile = ' calls.txt ' , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' ), title = ' Cell Hashing For Experiment 1 ' ) Installation # Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile: local({options(repos = BiocManager::repositories())}) #Latest version: devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'master', dependencies = TRUE, upgrade = 'always') Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page . We recommend using a specific release, which you can do using tags: docker pull ghcr.io/bimberlab/cellhashr:latest Known Issues If you receive an error along the lines of: "ERROR; return code from pthread_create() is 22\n" Please manually install preprocessCore with threading disabled: devtools::install_github('bmbolstad/preprocessCore', dependencies = T, upgrade = 'always', configure.args = '--disable-threading') Providing h5 file to demuxEM/demuxmix Unlike the other algorithms, which just require the HTO count matrix, demuxEM and demuxmix also require the path to the 10x h5 gene expression counts. This can be supplied as follows. This example runs BFF and demuxEM: rawData &lt;- '../testdata/438-21-GEX/umi_count' h5File &lt;- '../testdata/438-21-GEX/438-21-raw_feature_bc_matrix.h5' barcodeMatrix &lt;- ProcessCountMatrix(rawCountData = rawData, barcodeWhitelist = c('MS-11', 'MS-12')) df &lt;- GenerateCellHashingCalls(barcodeMatrix = barcodeMatrix, methods = c('bff_cluster', 'demuxem'), rawFeatureMatrixH5 = h5File) Development Guidelines New development should occur on a branch, and go through a Pull Request before merging into the master branch. See here for information on the pull request workflow . Ideally PRs would be reviewed by another person. For the PR, please review the set of changed files carefully to make sure you are only merging the changes you intend. New functions should have Roxygen2 documentation . As part of each PR, you should run 'devtools::document()' to update documentation and include these changes with your commits. It is a good idea to run 'R CMD check' locally to make sure your changes will pass. See here for more information Code should only be merged after the build and tests pass. The master branch should always be stable. New features should ideally have at least a basic test (see R testthat ). There is existing test data in ./tests/testdata. This can be expanded, but please be conscious about file size and try to reuse data across tests if appropriate. About An R package designed to demultiplex cell hashing data Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 31 stars Watchers 3 watching Forks 8 forks Report repository Releases 4 Version 1.2.1 Latest Mar 15, 2025 + 3 releases Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 99.4% Dockerfile 0.6% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+### https://github.com/BimberLab/cellhashR
+GitHub - BimberLab/cellhashR: An R package designed to demultiplex cell hashing data · GitHub Skip to content Navigation Menu Toggle navigation Sign in Appearance settings Platform AI CODE CREATION GitHub Copilot Write better code with AI GitHub Spark Build and deploy intelligent apps GitHub Models Manage and compare prompts MCP Registry New Integrate external tools DEVELOPER WORKFLOWS Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes APPLICATION SECURITY GitHub Advanced Security Find and fix vulnerabilities Code security Secure your code as you build Secret protection Stop leaks before they start EXPLORE Why GitHub Documentation Blog Changelog Marketplace View all features Solutions BY COMPANY SIZE Enterprises Small and medium teams Startups Nonprofits BY USE CASE App Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRY Healthcare Financial services Manufacturing Government View all industries View all solutions Resources EXPLORE BY TOPIC AI Software Development DevOps Security View all topics EXPLORE BY TYPE Customer stories Events &amp; webinars Ebooks &amp; reports Business insights GitHub Skills SUPPORT &amp; SERVICES Documentation Customer support Community forum Trust center Partners View all resources Open Source COMMUNITY GitHub Sponsors Fund open source developers PROGRAMS Security Lab Maintainer Community Accelerator GitHub Stars Archive Program REPOSITORIES Topics Trending Collections Enterprise ENTERPRISE SOLUTIONS Enterprise platform AI-powered developer platform AVAILABLE ADD-ONS GitHub Advanced Security Enterprise-grade security features Copilot for Business Enterprise-grade AI features Premium Support Enterprise-grade 24/7 support Pricing Search or jump to... Search code, repositories, users, issues, pull requests... --> Search Clear Search syntax tips Provide feedback --> We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your results more quickly --> Name Query To see all available qualifiers, see our documentation . Cancel Create saved search Sign in Sign up Appearance settings Resetting focus You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session. Dismiss alert {{ message }} BimberLab / cellhashR Public Notifications You must be signed in to change notification settings Fork 8 Star 31 Code Issues 0 Pull requests 0 Actions Security and quality 0 Insights Additional navigation options Code Issues Pull requests Actions Security and quality Insights BimberLab/cellhashR master Branches Tags Go to file Code Open more actions menu Folders and files Name Name Last commit message Last commit date Latest commit History 224 Commits 224 Commits .github .github R R inst/ rmd inst/ rmd man man tests tests vignettes vignettes .Rbuildignore .Rbuildignore .dockerignore .dockerignore .gitignore .gitignore DESCRIPTION DESCRIPTION Dockerfile Dockerfile NAMESPACE NAMESPACE README.md README.md _pkgdown.yml _pkgdown.yml cellhashR.iml cellhashR.iml View all files Repository files navigation README cellhashR An R package designed to demultiplex cell hashing data. Please see our documentation for more detail . Table of Contents Overview Example Usage Installation Known Issues Development Guidelines Overview Cell hashing is a method that allows sample multiplexing or super-loading within single-cell RNA-seq platforms, such as 10x genomics, originally developed at New York Genome Center in collaboration with the Satija lab. See here for more detail on the technique . The general idea is that cells are labeled with a staining reagent (such as an antibody) tagged with a short nucleotide barcode. Other staining methods have been published, such as the lipid-based Multi-Seq ( https://www.ncbi.nlm.nih.gov/pubmed/31209384 ). In all methods, the hashtag oligo/barcode is sequenced in parallel with cellular mRNA, creating a separate cell hashing library. After sequencing, the cell barcode and hashing index are parsed using tools like Cite-seq-Count ( https://github.com/Hoohm/CITE-seq-Count ), creating a count matrix with the total hash tag counts per cell. Once the count matrix is created, an algorithm must be used to demultiplex cells and assign them to hash tags (i.e. sample). This is where cellhashR comes in. This package provides several functions: Quality control reports for the cell hashing library, covering read counts and normalization. Think FASTQC , except for cell hashing data. A single interface to run one or more demutiplexing algorithms, including the novel demultiplexing algorithms BFF_raw and BFF_cluster. Each algorithm has pros and cons, and will perform better or worse under certain conditions (though in our experience, of the algorithms we have tested, the BFF algorithms work most consistently and under the widest variety of conditions). If you select multiple algorithms (our default workflow), cellhashR will score cells using the consensus call from the set. Various QC summaries are produced during this process as well, if debugging is needed. In addition to the BFF demultiplexing algorithms, other algorithms that can be run from cellhashR include: GMM-Demux demuxEM (see extra requirements below) demuxmix (see extra requirements below) deMULTIplex HTODemux from Seurat hashedDrops from DropletUtils The workflow produces a unified table with the results of each caller and the consensus call. Final QC plots and summaries are created. Each step of the workflow can either be run interactively in R (through the terminal or RStudio), or it can be executed as a pipeline that runs all commands and creates the call table and an HTML report. Click here to view an example QC report Consensus Calling In addition to allowing one to run multiple demuliplexing algorithms to compare results, cellhashR can generate a consensus call based on those scores. This can be useful, since some algorithms will perform better or worse under some conditions. This is automatically built into the dataframe returned by GenerateCellHashingCalls(). Some additional parameters that might be worth considering are: There are separate arguments for 'methods' (i.e. which algorithms will be run), and 'methodsForConsensus', which determined the subset that will be used for the consensus call. majorityConsensusThreshold: This applies to calculating a consensus call when multiple algorithms are used. If NULL, then all non-negative calls must agree or that cell is marked discordant. If non-NULL, then the number of algorithms returning the top call is divided by the total number of non-negative calls. If this ratio is above the majorityConsensusThreshold, that value is selected. For example, when majorityConsensusThreshold=0.6 and the calls are: HTO-1,HTO-1,Negative,HTO-2, then 2/3 calls are for HTO-1, giving 0.66. This is greater than the majorityConsensusThreshold of 0.6, so HTO-1 is returned. This can be useful for situations where most algorithms agree, but a single caller fails. callerDisagreementThreshold: If provided, the agreement rate will be calculated between each caller and the simple majority call, ignoring discordant and no-call cells. If any caller has an disagreement rate above this threshold, it will be dropped and the consensus call re-calculated. The general idea is to drop a caller that is systematically discordant. Example Usage Below are the primary functions of cellhashR needed to QC and score hashing data: # Example 1: parse CITE-seq-Count output, printing QC barcodeData &lt;- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 ) # Example 2: parse CITE-seq-Count output, providing a barcode whitelist. barcodeData &lt;- ProcessCountMatrix( rawCountData = ' myCountDir/umi_count ' , minCountPerCell = 5 , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' , ' HTO-4 ' , ' HTO-6 ' )) # Create QC plots of barcode normalization PlotNormalizationQC( barcodeData ) # Generate the final cell hashing calls calls &lt;- GenerateCellHashingCalls( barcodeMatrix = barcodeData , methods = c( ' multiseq ' , ' htodemux ' )) # Inspect negative cells: SummarizeCellsByClassification( calls = calls , barcodeMatrix = barcodeData ) Or export/save a template RMarkdown file outlining the default workflow, which can be run interactively or headlessly as part of a pipeline: GetExampleMarkdown( dest = ' cellhashR_template.rmd ' ) Finally, the workflow can be executed using this wrapper around the Rmarkdown, producing a TSV of calls and HTML QC report: CallAndGenerateReport( rawCountData = ' myCountDir/umi_count ' , reportFile = ' report.html ' , callFile = ' calls.txt ' , barcodeWhitelist = c( ' HTO-1 ' , ' HTO-2 ' , ' HTO-3 ' ), title = ' Cell Hashing For Experiment 1 ' ) Installation # Make sure to update your Rprofile to include Bioconductor repos, such as adding this line to ~/.Rprofile: local({options(repos = BiocManager::repositories())}) #Latest version: devtools::install_github(repo = 'bimberlab/cellhashR', ref = 'master', dependencies = TRUE, upgrade = 'always') Pre-packaged Docker images with all needed dependencies installed can be found on our GitHub Packages page . We recommend using a specific release, which you can do using tags: docker pull ghcr.io/bimberlab/cellhashr:latest Known Issues If you receive an error along the lines of: "ERROR; return code from pthread_create() is 22\n" Please manually install preprocessCore with threading disabled: devtools::install_github('bmbolstad/preprocessCore', dependencies = T, upgrade = 'always', configure.args = '--disable-threading') Providing h5 file to demuxEM/demuxmix Unlike the other algorithms, which just require the HTO count matrix, demuxEM and demuxmix also require the path to the 10x h5 gene expression counts. This can be supplied as follows. This example runs BFF and demuxEM: rawData &lt;- '../testdata/438-21-GEX/umi_count' h5File &lt;- '../testdata/438-21-GEX/438-21-raw_feature_bc_matrix.h5' barcodeMatrix &lt;- ProcessCountMatrix(rawCountData = rawData, barcodeWhitelist = c('MS-11', 'MS-12')) df &lt;- GenerateCellHashingCalls(barcodeMatrix = barcodeMatrix, methods = c('bff_cluster', 'demuxem'), rawFeatureMatrixH5 = h5File) Development Guidelines New development should occur on a branch, and go through a Pull Request before merging into the master branch. See here for information on the pull request workflow . Ideally PRs would be reviewed by another person. For the PR, please review the set of changed files carefully to make sure you are only merging the changes you intend. New functions should have Roxygen2 documentation . As part of each PR, you should run 'devtools::document()' to update documentation and include these changes with your commits. It is a good idea to run 'R CMD check' locally to make sure your changes will pass. See here for more information Code should only be merged after the build and tests pass. The master branch should always be stable. New features should ideally have at least a basic test (see R testthat ). There is existing test data in ./tests/testdata. This can be expanded, but please be conscious about file size and try to reuse data across tests if appropriate. About An R package designed to demultiplex cell hashing data Resources Readme Uh oh! There was an error while loading. Please reload this page . Activity Custom properties Stars 31 stars Watchers 3 watching Forks 8 forks Report repository Releases 4 Version 1.2.1 Latest Mar 15, 2025 + 3 releases Packages 0 &nbsp; &nbsp; &nbsp; Uh oh! There was an error while loading. Please reload this page . Uh oh! There was an error while loading. Please reload this page . Contributors Uh oh! There was an error while loading. Please reload this page . Languages R 99.4% Dockerfile 0.6% Footer &copy; 2026 GitHub,&nbsp;Inc. Footer navigation Terms Privacy Security Status Community Docs Contact Manage cookies Do not share my personal information You can’t perform that action at this time.
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-cellhashr --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-cellhashr 1.04 r43hdfd78af_0
+-----------------------------------------
+file name   : bioconductor-cellhashr-1.04-r43hdfd78af_0.tar.bz2
+name        : bioconductor-cellhashr
+version     : 1.04
+build       : r43hdfd78af_0
+build number: 0
+size        : 260 KB
+license     : MIT
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-cellhashr-1.04-r43hdfd78af_0.tar.bz2
+md5         : e51ecc711bcadf09a6bbd573b87d1f41
+timestamp   : 2024-04-01 06:41:15 UTC
+dependencies: 
+  - bioconductor-demuxmix
+  - bioconductor-dropletutils
+  - bioconductor-nempi
+  - bioconductor-preprocesscore
+  - r-base >=4.3,<4.4.0a0
+  - r-devtools
+  - r-egg
+  - r-essentials
+  - r-ggextra
+  - r-ggforce
+  - r-ggthemes
+  - r-patchwork
+  - r-rcpp
+  - r-rcpparmadillo
+  - r-rcppeigen
+  - r-rcppparallel
+  - r-rcppprogress
+  - r-reticulate
+  - r-rmdformats
+  - r-seurat
+  - r-seuratobject

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ctsv.manual_bundle.txt

@@ -0,0 +1,138 @@
+# Tool: bioconductor-ctsv
+software_name: bioconductor-ctsv
+tier: T1
+domain: spatial_transcriptomics
+downloads: 5480
+summary: Identification of cell-type-specific spatially variable genes accounting for excess zeros
+description: The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-qvalue >=2.42.0,<2.43.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-knitr, r-pscl
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.16/bioc/html/CTSV.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.16/bioc/html/CTSV.html
+Bioconductor - CTSV About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages CTSV CTSV This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CTSV . Identification of cell-type-specific spatially variable genes accounting for excess zeros DOI: 10.18129/B9.bioc.CTSV Bioconductor version: 3.16 The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS. Author: Jinge Yu Developer [aut, cre], Xiangyu Luo Developer [aut] Maintainer: Jinge Yu Developer &#x3c;&#x79;&#x6a;&#x67;&#x72;&#x75;&#x63;&#x20;&#x61;&#x74;&#x20;&#x72;&#x75;&#x63;&#x2e;&#x65;&#x64;&#x75;&#x2e;&#x63;&#x6e;&#x3e; Citation (from within R, enter citation("CTSV") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CTSV") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("CTSV") Basic Usage HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GeneExpression , Genetics , Regression , Software , Spatial , StatisticalMethod Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License GPL-3 Depends R (>= 4.2) Imports stats, pscl, qvalue , BiocParallel , methods, knitr, SpatialExperiment , SummarizedExperiment System Requirements URL https://github.com/jingeyu/CTSV Bug Reports https://github.com/jingeyu/CTSV/issues See More Suggests testthat, BiocStyle Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package CTSV_1.0.0.tar.gz Windows Binary CTSV_1.0.0.zip macOS Binary (x86_64) CTSV_1.0.0.tgz macOS Binary (arm64) CTSV_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/CTSV Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CTSV Bioc Package Browser https://code.bioconductor.org/browse/CTSV/ Package Short Url https://bioconductor.org/packages/CTSV/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-ctsv --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-ctsv 1.0.0 r42hdfd78af_0
+-------------------------------------
+file name   : bioconductor-ctsv-1.0.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-ctsv
+version     : 1.0.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 333 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.0.0-r42hdfd78af_0.tar.bz2
+md5         : 477e92194b308953418ec2d1b48b3837
+timestamp   : 2022-11-06 01:40:28 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.32.0,<1.33.0
+  - bioconductor-qvalue >=2.30.0,<2.31.0
+  - bioconductor-spatialexperiment >=1.8.0,<1.9.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - r-base >=4.2,<4.3.0a0
+  - r-knitr
+  - r-pscl
+
+
+bioconductor-ctsv 1.2.0 r43hdfd78af_0
+-------------------------------------
+file name   : bioconductor-ctsv-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-ctsv
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 336 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : c0e412661c7c2a8aafcaacac687e34da
+timestamp   : 2023-07-16 16:05:22 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-qvalue >=2.32.0,<2.33.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - r-base >=4.3,<4.4.0a0
+  - r-knitr
+  - r-pscl
+
+
+bioconductor-ctsv 1.4.0 r43hdfd78af_0
+-------------------------------------
+file name   : bioconductor-ctsv-1.4.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-ctsv
+version     : 1.4.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 344 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.4.0-r43hdfd78af_0.tar.bz2
+md5         : 8831b06fb052b21f542c519d0da9e33f
+timestamp   : 2023-12-07 00:49:18 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-qvalue >=2.34.0,<2.35.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - r-base >=4.3,<4.4.0a0
+  - r-knitr
+  - r-pscl
+
+
+bioconductor-ctsv 1.8.0 r44hdfd78af_0
+-------------------------------------
+file name   : bioconductor-ctsv-1.8.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-ctsv
+version     : 1.8.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 346 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.8.0-r44hdfd78af_0.tar.bz2
+md5         : 3a7349d1f0d0c4125aacdcad2d371fbd
+timestamp   : 2024-12-22 16:20:01 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-qvalue >=2.38.0,<2.39.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - r-base >=4.4,<4.5.0a0
+  - r-knitr
+  - r-pscl
+
+
+bioconductor-ctsv 1.12.0 r45hdfd78af_0
+--------------------------------------
+file name   : bioconductor-ctsv-1.12.0-r45hdfd78af_0.conda
+name        : bioconductor-ctsv
+version     : 1.12.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 318 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ctsv-1.12.0-r45hdfd78af_0.conda
+md5         : 19db14a69bfd3414d69c779b9e87a337
+timestamp   : 2026-03-01 23:21:39 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-qvalue >=2.42.0,<2.43.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-base >=4.5,<4.6.0a0
+  - r-knitr
+  - r-pscl

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-decontam.manual_bundle.txt

@@ -0,0 +1,327 @@
+# Tool: bioconductor-decontam
+software_name: bioconductor-decontam
+tier: T1
+domain: t1_backfill_overall
+downloads: 207011
+summary: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
+description: Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.
+dependencies: r-base >=4.5,<4.6.0a0, r-ggplot2 >=2.1.0, r-reshape2 >=1.4.1
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.7/bioc/html/decontam.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.7/bioc/html/decontam.html
+Bioconductor - decontam About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.7 Software Packages decontam decontam This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see decontam . Identify Contaminants in Marker-gene and Metagenomics Sequencing Data DOI: 10.18129/B9.bioc.decontam Bioconductor version: 3.7 Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples. Author: Benjamin Callahan &#x3c;&#x62;&#x65;&#x6e;&#x6a;&#x61;&#x6d;&#x69;&#x6e;&#x2e;&#x6a;&#x2e;&#x63;&#x61;&#x6c;&#x6c;&#x61;&#x68;&#x61;&#x6e;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e;, Nicole Marie Davis Maintainer: Benjamin Callahan &#x3c;&#x62;&#x65;&#x6e;&#x6a;&#x61;&#x6d;&#x69;&#x6e;&#x2e;&#x6a;&#x2e;&#x63;&#x61;&#x6c;&#x6c;&#x61;&#x68;&#x61;&#x6e;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("decontam") ): Installation To install this package, start R (version "3.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("decontam") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("decontam") Introduction to dada2 HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Classification , Metagenomics , Microbiome , Sequencing , Software Version 1.0.0 In Bioconductor since BioC 3.7 (R-3.5) (6 years) License Artistic-2.0 Depends R (>= 3.4.1), methods (>= 3.4.1) Imports ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats System Requirements URL https://github.com/benjjneb/decontam Bug Reports https://github.com/benjjneb/decontam/issues See More Suggests BiocStyle , knitr, rmarkdown, phyloseq Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package decontam_1.0.0.tar.gz Windows Binary decontam_1.0.0.zip Mac OS X 10.11 (El Capitan) decontam_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/decontam Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decontam Package Short Url https://bioconductor.org/packages/decontam/ Package Downloads Report Download Stats Old Source Packages for BioC 3.7 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-decontam --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-decontam 1.0.0 r351_0
+----------------------------------
+file name   : bioconductor-decontam-1.0.0-r351_0.tar.bz2
+name        : bioconductor-decontam
+version     : 1.0.0
+build       : r351_0
+build number: 0
+size        : 699 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.0.0-r351_0.tar.bz2
+md5         : 4516715a362019afec2e32847850075e
+timestamp   : 2018-12-19 02:04:58 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.2.1 r351_0
+----------------------------------
+file name   : bioconductor-decontam-1.2.1-r351_0.tar.bz2
+name        : bioconductor-decontam
+version     : 1.2.1
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+build number: 0
+size        : 733 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.2.1-r351_0.tar.bz2
+md5         : 82baedd84cfe6053bbda25425c1d71f7
+timestamp   : 2019-01-09 11:44:37 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.4.0 r351_0
+----------------------------------
+file name   : bioconductor-decontam-1.4.0-r351_0.tar.bz2
+name        : bioconductor-decontam
+version     : 1.4.0
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+build number: 0
+size        : 737 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.4.0-r351_0.tar.bz2
+md5         : b4e2ba0ea639069277d5f7ebc361b92b
+timestamp   : 2019-05-11 18:40:18 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.4.0 r36_1
+---------------------------------
+file name   : bioconductor-decontam-1.4.0-r36_1.tar.bz2
+name        : bioconductor-decontam
+version     : 1.4.0
+build       : r36_1
+build number: 1
+size        : 733 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.4.0-r36_1.tar.bz2
+md5         : 60c7bd9f5bef618e8f44736cd663ad11
+timestamp   : 2019-07-18 11:00:39 UTC
+dependencies: 
+  - r-base >=3.6,<3.7.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.6.0 r36_0
+---------------------------------
+file name   : bioconductor-decontam-1.6.0-r36_0.tar.bz2
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+version     : 1.6.0
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+build number: 0
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.6.0-r36_0.tar.bz2
+md5         : df2a20bd4411caa28717a6836e587627
+timestamp   : 2019-11-01 12:39:59 UTC
+dependencies: 
+  - r-base >=3.6,<3.7.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.8.0 r40_0
+---------------------------------
+file name   : bioconductor-decontam-1.8.0-r40_0.tar.bz2
+name        : bioconductor-decontam
+version     : 1.8.0
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+md5         : 526ad6016a7a80055a0c2620a5d1ffe0
+timestamp   : 2020-05-09 14:32:20 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.10.0 r40_0
+----------------------------------
+file name   : bioconductor-decontam-1.10.0-r40_0.tar.bz2
+name        : bioconductor-decontam
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+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.10.0-r40_0.tar.bz2
+md5         : 67337ebc1b845ae2ae37e0959f9eac53
+timestamp   : 2020-10-29 16:55:23 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.10.0 r40hdfd78af_1
+------------------------------------------
+file name   : bioconductor-decontam-1.10.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-decontam
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+build       : r40hdfd78af_1
+build number: 1
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.10.0-r40hdfd78af_1.tar.bz2
+md5         : 4b7dce05cbf0ae1bd7eda260986840b8
+timestamp   : 2021-03-25 19:48:06 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.12.0 r41hdfd78af_0
+------------------------------------------
+file name   : bioconductor-decontam-1.12.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-decontam
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+build number: 0
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.12.0-r41hdfd78af_0.tar.bz2
+md5         : 18e7e0eb2754f63ecc37fed96d37d8c9
+timestamp   : 2021-05-30 21:26:54 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
+
+
+bioconductor-decontam 1.14.0 r41hdfd78af_0
+------------------------------------------
+file name   : bioconductor-decontam-1.14.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-decontam
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+build number: 0
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-decontam-1.14.0-r41hdfd78af_0.tar.bz2
+md5         : 8a8467938a79304d74f3edff935f7cce
+timestamp   : 2021-11-01 15:36:02 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-ggplot2 >=2.1.0
+  - r-reshape2 >=1.4.1
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+
+bioconductor-decontam 1.18.0 r42hdfd78af_0
+------------------------------------------
+file name   : bioconductor-decontam-1.18.0-r42hdfd78af_0.tar.bz2
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+md5         : 9398479e9b8c9d06bd3fd3e8f0041433
+timestamp   : 2022-11-03 08:02:49 UTC
+dependencies: 
+  - r-base >=4.2,<4.3.0a0
+  - r-ggplot2 >=2.1.0
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+
+bioconductor-decontam 1.20.0 r43hdfd78af_0
+------------------------------------------
+file name   : bioconductor-decontam-1.20.0-r43hdfd78af_0.tar.bz2
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+timestamp   : 2023-07-07 08:07:46 UTC
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+  - r-ggplot2 >=2.1.0
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+
+bioconductor-decontam 1.22.0 r43hdfd78af_0
+------------------------------------------
+file name   : bioconductor-decontam-1.22.0-r43hdfd78af_0.tar.bz2
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+dependencies: 
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+  - r-ggplot2 >=2.1.0
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+------------------------------------------
+file name   : bioconductor-decontam-1.26.0-r44hdfd78af_0.tar.bz2
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+dependencies: 
+  - r-base >=4.5,<4.6.0a0
+  - r-ggplot2 >=2.1.0
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+
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+------------------------------------------
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+dependencies: 
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+  - r-reshape2 >=1.4.1

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-deconvobuddies.manual_bundle.txt

@@ -0,0 +1,58 @@
+# Tool: bioconductor-deconvobuddies
+software_name: bioconductor-deconvobuddies
+tier: T1
+domain: spatial_transcriptomics
+downloads: 31
+summary: Helper Functions for LIBD Deconvolution
+description: Funtions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets.
+dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-biocfilecache >=3.0.0,<3.1.0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scran >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatiallibd >=1.22.0,<1.23.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggplot2, r-purrr, r-rafalib, r-reshape2, r-stringr, r-tibble
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/DeconvoBuddies.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/DeconvoBuddies.html
+Bioconductor - DeconvoBuddies Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages DeconvoBuddies DeconvoBuddies This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see DeconvoBuddies . Helper Functions for LIBD Deconvolution DOI: 10.18129/B9.bioc.DeconvoBuddies Bioconductor version: 3.22 Funtions helpful for LIBD deconvolution project. Includes tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results. Working to include DLPFC datasets. Author: Louise Huuki-Myers [aut, cre] ORCID: 0000-0001-5148-3602 , Leonardo Collado-Torres [ctb] ORCID: 0000-0003-2140-308X Maintainer: Louise Huuki-Myers &#x3c;&#x6c;&#x61;&#x68;&#x75;&#x75;&#x6b;&#x69;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("DeconvoBuddies") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DeconvoBuddies") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DeconvoBuddies") Deconvolution Benchmark in Human DLPFC HTML R Script Finding Marker Genes with DeconvoBuddies HTML R Script Get Started with DeconvoBuddies HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentHubSoftware , GeneExpression , RNASeq , SingleCell , Software , Transcriptomics Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License Artistic-2.0 Depends R (>= 4.4.0) Imports AnnotationHub , BiocFileCache , DelayedMatrixStats , dplyr , ExperimentHub , ggplot2 , graphics, grDevices, MatrixGenerics , methods, purrr , rafalib , reshape2 , S4Vectors , scran , SingleCellExperiment , spatialLIBD , stats, stringr , SummarizedExperiment , tibble , utils System Requirements URL https://github.com/lahuuki/DeconvoBuddies Bug Reports https://github.com/LieberInstitute/DeconvoBuddies/issues See More Suggests Biobase , BiocStyle , covr , HDF5Array , knitr , RColorBrewer , RefManageR , rmarkdown , sessioninfo , testthat (>= 3.0.0), tidyr , tidyverse Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DeconvoBuddies_1.2.0.tar.gz Windows Binary (x86_64) DeconvoBuddies_1.2.0.zip macOS Binary (x86_64) DeconvoBuddies_1.2.0.tgz macOS Binary (arm64) DeconvoBuddies_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DeconvoBuddies Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DeconvoBuddies Bioc Package Browser https://code.bioconductor.org/browse/DeconvoBuddies/ Package Short Url https://bioconductor.org/packages/DeconvoBuddies/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-deconvobuddies --info
+[rc=0]
+2 channel Terms of Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-deconvobuddies 1.2.0 r45hdfd78af_0
+-----------------------------------------------
+file name   : bioconductor-deconvobuddies-1.2.0-r45hdfd78af_0.conda
+name        : bioconductor-deconvobuddies
+version     : 1.2.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 5.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-deconvobuddies-1.2.0-r45hdfd78af_0.conda
+md5         : 77de41c166da27b1831eec7cd31f6f4f
+timestamp   : 2026-03-03 07:09:18 UTC
+dependencies: 
+  - bioconductor-annotationhub >=4.0.0,<4.1.0
+  - bioconductor-biocfilecache >=3.0.0,<3.1.0
+  - bioconductor-delayedmatrixstats >=1.32.0,<1.33.0
+  - bioconductor-experimenthub >=3.0.0,<3.1.0
+  - bioconductor-matrixgenerics >=1.22.0,<1.23.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-scran >=1.38.0,<1.39.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatiallibd >=1.22.0,<1.23.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-base >=4.5,<4.6.0a0
+  - r-dplyr
+  - r-ggplot2
+  - r-purrr
+  - r-rafalib
+  - r-reshape2
+  - r-stringr
+  - r-tibble

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-delayedmatrixstats.manual_bundle.txt

@@ -0,0 +1,343 @@
+# Tool: bioconductor-delayedmatrixstats
+software_name: bioconductor-delayedmatrixstats
+tier: T1
+domain: t1_backfill_overall
+downloads: 536481
+summary: Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
+description: A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.
+dependencies: bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-sparsearray >=1.10.0,<1.11.0, bioconductor-sparsematrixstats >=1.22.0,<1.23.0, r-base >=4.5,<4.6.0a0, r-matrix >=1.5-0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: http://bioconductor.org/packages/3.7/bioc/html/DelayedMatrixStats.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### http://bioconductor.org/packages/3.7/bioc/html/DelayedMatrixStats.html
+Bioconductor - DelayedMatrixStats About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.7 Software Packages DelayedMatrixStats DelayedMatrixStats This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see DelayedMatrixStats . Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects DOI: 10.18129/B9.bioc.DelayedMatrixStats Bioconductor version: 3.7 A port of the 'matrixStats' API for use with DelayedMatrix objects from the 'DelayedArray' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. Author: Peter Hickey &#x3c;&#x70;&#x65;&#x74;&#x65;&#x72;&#x2e;&#x68;&#x69;&#x63;&#x6b;&#x65;&#x79;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Maintainer: Peter Hickey &#x3c;&#x70;&#x65;&#x74;&#x65;&#x72;&#x2e;&#x68;&#x69;&#x63;&#x6b;&#x65;&#x79;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("DelayedMatrixStats") ): Installation To install this package, start R (version "3.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DelayedMatrixStats") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DelayedMatrixStats") Overview of DelayedMatrixStats HTML R Script Reference Manual PDF LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 1.2.0 In Bioconductor since BioC 3.6 (R-3.4) (6.5 years) License MIT + file LICENSE Depends DelayedArray (>= 0.5.27) Imports methods, matrixStats (>= 0.53.1), Matrix, S4Vectors (>= 0.17.5), IRanges System Requirements URL https://github.com/PeteHaitch/DelayedMatrixStats Bug Reports https://github.com/PeteHaitch/DelayedMatrixStats/issues See More Suggests testthat, HDF5Array (>= 1.7.10), knitr, rmarkdown, covr, BiocStyle , microbenchmark, profmem Linking To Enhances Depends On Me Imports Me bsseq , dmrseq , minfi , scater , scran Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DelayedMatrixStats_1.2.0.tar.gz Windows Binary DelayedMatrixStats_1.2.0.zip Mac OS X 10.11 (El Capitan) DelayedMatrixStats_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DelayedMatrixStats Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DelayedMatrixStats Package Short Url https://bioconductor.org/packages/DelayedMatrixStats/ Package Downloads Report Download Stats Old Source Packages for BioC 3.7 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-delayedmatrixstats --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-delayedmatrixstats 1.2.0 r341_0
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.2.0-r341_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.2.0
+build       : r341_0
+build number: 0
+size        : 621 KB
+license     : MIT + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-delayedmatrixstats-1.2.0-r341_0.tar.bz2
+md5         : 4e85c5354071920cccc475a74a6d1789
+timestamp   : 2018-10-12 13:28:28 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.6.6,<0.8.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.53.1
+
+
+bioconductor-delayedmatrixstats 1.2.0 r351_0
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.2.0-r351_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.2.0
+build       : r351_0
+build number: 0
+size        : 709 KB
+license     : MIT + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-delayedmatrixstats-1.2.0-r351_0.tar.bz2
+md5         : c833de95106231ae6f4c86894531b018
+timestamp   : 2018-10-12 13:26:47 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.6.6,<0.8.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.53.1
+
+
+bioconductor-delayedmatrixstats 1.4.0 r351_0
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.4.0-r351_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.4.0
+build       : r351_0
+build number: 0
+size        : 712 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.4.0-r351_0.tar.bz2
+md5         : 5da706b3b1a6104cc8648050ad575668
+timestamp   : 2018-12-11 16:30:24 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.16.0,<1.17.0
+  - bioconductor-delayedarray >=0.8.0,<0.9.0
+  - bioconductor-hdf5array >=1.10.0,<1.11.0
+  - bioconductor-iranges >=2.16.0,<2.17.0
+  - bioconductor-s4vectors >=0.20.0,<0.21.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.53.1
+
+
+bioconductor-delayedmatrixstats 1.4.0 r351_1
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.4.0-r351_1.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.4.0
+build       : r351_1
+build number: 1
+size        : 712 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.4.0-r351_1.tar.bz2
+md5         : 7608a4f8816eb8ad7c26f5d07c299a22
+timestamp   : 2019-03-10 12:41:02 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.16.0,<1.17.0
+  - bioconductor-delayedarray >=0.8.0,<0.9.0
+  - bioconductor-hdf5array >=1.10.0,<1.11.0
+  - bioconductor-iranges >=2.16.0,<2.17.0
+  - bioconductor-s4vectors >=0.20.0,<0.21.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.53.1
+
+
+bioconductor-delayedmatrixstats 1.6.0 r36_1
+-------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.6.0-r36_1.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.6.0
+build       : r36_1
+build number: 1
+size        : 695 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.6.0-r36_1.tar.bz2
+md5         : 8f24604d354147fca84733626ba31c2d
+timestamp   : 2019-07-24 16:18:36 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.18.0,<1.19.0
+  - bioconductor-delayedarray >=0.10.0,<0.11.0
+  - bioconductor-hdf5array >=1.12.0,<1.13.0
+  - bioconductor-iranges >=2.18.0,<2.19.0
+  - bioconductor-s4vectors >=0.22.0,<0.23.0
+  - r-base >=3.6,<3.7.0a0
+  - r-matrix
+  - r-matrixstats >=0.53.1
+
+
+bioconductor-delayedmatrixstats 1.8.0 r36_0
+-------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.8.0-r36_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.8.0
+build       : r36_0
+build number: 0
+size        : 712 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.8.0-r36_0.tar.bz2
+md5         : 52f864c3627f6cddb8581d9c9b22c0e7
+timestamp   : 2019-11-03 17:54:02 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.20.0,<1.21.0
+  - bioconductor-delayedarray >=0.12.0,<0.13.0
+  - bioconductor-hdf5array >=1.14.0,<1.15.0
+  - bioconductor-iranges >=2.20.0,<2.21.0
+  - bioconductor-s4vectors >=0.24.0,<0.25.0
+  - r-base >=3.6,<3.7.0a0
+  - r-matrix
+  - r-matrixstats >=0.55.0
+
+
+bioconductor-delayedmatrixstats 1.10.0 r40_0
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.10.0-r40_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.10.0
+build       : r40_0
+build number: 0
+size        : 720 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.10.0-r40_0.tar.bz2
+md5         : e39dd812ab80f634c0205387cb02358f
+timestamp   : 2020-05-10 06:12:20 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.22.0,<1.23.0
+  - bioconductor-delayedarray >=0.14.0,<0.15.0
+  - bioconductor-hdf5array >=1.16.0,<1.17.0
+  - bioconductor-iranges >=2.22.0,<2.23.0
+  - bioconductor-s4vectors >=0.26.0,<0.27.0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-delayedmatrixstats 1.12.0 r40_0
+--------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.12.0-r40_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.12.0
+build       : r40_0
+build number: 0
+size        : 700 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.12.0-r40_0.tar.bz2
+md5         : c960ae00e16989b0743bf9e24675b03d
+timestamp   : 2020-10-30 12:46:01 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-hdf5array >=1.18.0,<1.19.0
+  - bioconductor-iranges >=2.24.0,<2.25.0
+  - bioconductor-matrixgenerics >=1.2.0,<1.3.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - bioconductor-sparsematrixstats >=1.2.0,<1.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-delayedmatrixstats 1.12.3 r40hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.12.3-r40hdfd78af_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.12.3
+build       : r40hdfd78af_0
+build number: 0
+size        : 705 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.12.3-r40hdfd78af_0.tar.bz2
+md5         : baf369164cc56e71688c59b84efc6d4e
+timestamp   : 2021-03-29 10:59:13 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-hdf5array >=1.18.0,<1.19.0
+  - bioconductor-iranges >=2.24.0,<2.25.0
+  - bioconductor-matrixgenerics >=1.2.0,<1.3.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - bioconductor-sparsematrixstats >=1.2.0,<1.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-delayedmatrixstats 1.14.0 r41hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.14.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.14.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 705 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.14.0-r41hdfd78af_0.tar.bz2
+md5         : 788fb46ff1acb3281fb1aaca0254c210
+timestamp   : 2021-06-01 01:22:21 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.18.0,<0.19.0
+  - bioconductor-iranges >=2.26.0,<2.27.0
+  - bioconductor-matrixgenerics >=1.4.0,<1.5.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - bioconductor-sparsematrixstats >=1.4.0,<1.5.0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-delayedmatrixstats 1.16.0 r41hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.16.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.16.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 729 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.16.0-r41hdfd78af_0.tar.bz2
+md5         : 7bfc1332d154df91e5b3fd71fbb4bf89
+timestamp   : 2021-11-03 11:17:18 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.20.0,<0.21.0
+  - bioconductor-iranges >=2.28.0,<2.29.0
+  - bioconductor-matrixgenerics >=1.6.0,<1.7.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-sparsematrixstats >=1.6.0,<1.7.0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+  - r-matrixstats >=0.60.0
+
+
+bioconductor-delayedmatrixstats 1.20.0 r42hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.20.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.20.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 722 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.20.0-r42hdfd78af_0.tar.bz2
+md5         : c303ba14d25cdd2ba0bca5a9f0914bf4
+timestamp   : 2022-11-04 14:23:43 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.24.0,<0.25.0
+  - bioconductor-iranges >=2.32.0,<2.33.0
+  - bioconductor-matrixgenerics >=1.10.0,<1.11.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - bioconductor-sparsematrixstats >=1.10.0,<1.11.0
+  - r-base >=4.2,<4.3.0a0
+  - r-matrix >=1.5-0
+  - r-matrixstats >=0.60.0
+
+
+bioconductor-delayedmatrixstats 1.22.1 r43hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.22.1-r43hdfd78af_0.tar.bz2
+name        : bioconductor-delayedmatrixstats
+version     : 1.22.1
+build       : r43hdfd78af_0
+build number: 0
+size        : 783 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-delayedmatrixstats-1.22.1-r43hdfd78af_0.tar.bz2
+md5         : c34a80ef52ed8e189a9903934ea06349
+timestamp   : 2023-07-11 09:02:58 UTC
+dependencies: 
+  - bioconductor-delayedarray >=0.26.0,<0.27.0
+  - bioconductor-iranges >=2.34.0,<2.35.0
+  - bioconductor-matrixgenerics >=1.12.0,<1.13.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-sparsematrixstats >=1.12.0,<1.13.0
+  - r-base >=4.3,<4.4.0a0
+  - r-matrix >=1.5-0
+  - r-matrixstats >=1.0.0
+
+
+bioconductor-delayedmatrixstats 1.24.0 r43hdfd78af_0
+----------------------------------------------------
+file name   : bioconductor-delayedmatrixstats-1.24.0-r43hdfd78af_0.tar.b

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-despace.manual_bundle.txt

@@ -0,0 +1,167 @@
+# Tool: bioconductor-despace
+software_name: bioconductor-despace
+tier: T1
+domain: spatial_transcriptomics
+downloads: 3385
+summary: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
+description: Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-edger >=4.8.0,<4.9.0, bioconductor-limma >=3.66.0,<3.67.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scuttle >=1.20.0,<1.21.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-assertthat, r-base >=4.5,<4.6.0a0, r-data.table, r-dplyr, r-ggforce, r-ggnewscale, r-ggplot2, r-matrix, r-patchwork, r-scales, r-sf, r-spatstat.explore, r-spatstat.geom, r-terra
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.17/bioc/html/DESpace.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.17/bioc/html/DESpace.html
+Bioconductor - DESpace About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages DESpace DESpace This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DESpace . DESpace: a framework to discover spatially variable genes DOI: 10.18129/B9.bioc.DESpace Bioconductor version: 3.17 Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates. Author: Peiying Cai [aut, cre] , Simone Tiberi [aut, cte] Maintainer: Peiying Cai &#x3c;&#x70;&#x65;&#x69;&#x79;&#x69;&#x6e;&#x67;&#x2e;&#x63;&#x61;&#x69;&#x20;&#x61;&#x74;&#x20;&#x75;&#x7a;&#x68;&#x2e;&#x63;&#x68;&#x3e; Citation (from within R, enter citation("DESpace") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESpace") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DESpace") A framework to discover spatially variable genes HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , GeneExpression , RNASeq , Sequencing , SingleCell , Software , Spatial , StatisticalMethod , Transcriptomics , Visualization Version 1.0.0 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License GPL-3 Depends R (>= 4.3.0) Imports edgeR , limma , dplyr, stats, Matrix, SpatialExperiment , ggplot2, ggpubr, scales, SummarizedExperiment , S4Vectors , BiocGenerics , data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel , methods System Requirements URL https://github.com/peicai/DESpace Bug Reports https://github.com/peicai/DESpace/issues See More Suggests knitr, rmarkdown, testthat, BiocStyle , ExperimentHub , concaveman, spatialLIBD , purrr, scuttle , utils Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DESpace_1.0.0.tar.gz Windows Binary DESpace_1.0.0.zip macOS Binary (x86_64) DESpace_1.0.0.tgz macOS Binary (arm64) DESpace_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DESpace Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DESpace Bioc Package Browser https://code.bioconductor.org/browse/DESpace/ Package Short Url https://bioconductor.org/packages/DESpace/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-despace --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-despace 1.0.0 r43hdfd78af_0
+----------------------------------------
+file name   : bioconductor-despace-1.0.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-despace
+version     : 1.0.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 3.7 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.0.0-r43hdfd78af_0.tar.bz2
+md5         : 4a2a753cf04467327bf250921da5d227
+timestamp   : 2023-07-16 01:34:09 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.46.0,<0.47.0
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-edger >=3.42.0,<3.43.0
+  - bioconductor-limma >=3.56.0,<3.57.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - r-assertthat
+  - r-base >=4.3,<4.4.0a0
+  - r-cowplot
+  - r-data.table
+  - r-dplyr
+  - r-ggforce
+  - r-ggnewscale
+  - r-ggplot2
+  - r-ggpubr
+  - r-matrix
+  - r-patchwork
+  - r-scales
+
+
+bioconductor-despace 1.2.0 r43hdfd78af_0
+----------------------------------------
+file name   : bioconductor-despace-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-despace
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 3.7 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : 2514f73704dd407706906068bd5ff879
+timestamp   : 2023-12-07 01:33:35 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.48.0,<0.49.0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-edger >=4.0.0,<4.1.0
+  - bioconductor-limma >=3.58.0,<3.59.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - r-assertthat
+  - r-base >=4.3,<4.4.0a0
+  - r-cowplot
+  - r-data.table
+  - r-dplyr
+  - r-ggforce
+  - r-ggnewscale
+  - r-ggplot2
+  - r-ggpubr
+  - r-matrix
+  - r-patchwork
+  - r-scales
+
+
+bioconductor-despace 1.6.0 r44hdfd78af_0
+----------------------------------------
+file name   : bioconductor-despace-1.6.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-despace
+version     : 1.6.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 3.7 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-1.6.0-r44hdfd78af_0.tar.bz2
+md5         : d4baa1ce08b5169f77409b0369918d46
+timestamp   : 2024-12-22 11:18:35 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.52.0,<0.53.0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-edger >=4.4.0,<4.5.0
+  - bioconductor-limma >=3.62.0,<3.63.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - r-assertthat
+  - r-base >=4.4,<4.5.0a0
+  - r-cowplot
+  - r-data.table
+  - r-dplyr
+  - r-ggforce
+  - r-ggnewscale
+  - r-ggplot2
+  - r-ggpubr
+  - r-matrix
+  - r-patchwork
+  - r-scales
+
+
+bioconductor-despace 2.2.2 r45h84498cf_0
+----------------------------------------
+file name   : bioconductor-despace-2.2.2-r45h84498cf_0.conda
+name        : bioconductor-despace
+version     : 2.2.2
+build       : r45h84498cf_0
+build number: 0
+size        : 6.8 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-despace-2.2.2-r45h84498cf_0.conda
+md5         : 476b0569f85ea1454930a979d484e158
+timestamp   : 2026-03-01 16:58:10 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.56.0,<0.57.0
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-edger >=4.8.0,<4.9.0
+  - bioconductor-limma >=3.66.0,<3.67.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-scuttle >=1.20.0,<1.21.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-assertthat
+  - r-base >=4.5,<4.6.0a0
+  - r-data.table
+  - r-dplyr
+  - r-ggforce
+  - r-ggnewscale
+  - r-ggplot2
+  - r-matrix
+  - r-patchwork
+  - r-scales
+  - r-sf
+  - r-spatstat.explore
+  - r-spatstat.geom
+  - r-terra

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-dnacopy.manual_bundle.txt

@@ -0,0 +1,412 @@
+# Tool: bioconductor-dnacopy
+software_name: bioconductor-dnacopy
+tier: T1
+domain: t1_backfill_overall
+downloads: 205182
+summary: DNA Copy Number Data Analysis
+description: Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.
+dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, libgfortran, libgfortran5 >=14.3.0, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/DNAcopy.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/DNAcopy.html
+Bioconductor - DNAcopy Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages DNAcopy DNAcopy This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see DNAcopy . DNA Copy Number Data Analysis DOI: 10.18129/B9.bioc.DNAcopy Bioconductor version: 3.22 Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. Author: Venkatraman E. Seshan, Adam Olshen Maintainer: Venkatraman E. Seshan &#x3c;&#x73;&#x65;&#x73;&#x68;&#x61;&#x6e;&#x76;&#x20;&#x61;&#x74;&#x20;&#x6d;&#x73;&#x6b;&#x63;&#x63;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("DNAcopy") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DNAcopy") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("DNAcopy") DNAcopy PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews CopyNumberVariation , Microarray , Software Version 1.84.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (&gt; 21 years) License GPL (>= 2) Depends Imports System Requirements URL See More Suggests Linking To Enhances Depends On Me CGHcall , cghMCR , CRImage , PureCN , CSclone , ParDNAcopy , saasCNV Imports Me ADaCGH2 , ChAMP , cn.farms , CNAnorm , CNVrd2 , conumee , GWASTools , maftools , MDTS , MEDIPS , MinimumDistance , QDNAseq , SCOPE , jointseg , PSCBS Suggests Me cn.mops , CopyNumberPlots , fastseg , nullranges , sesame , ACNE , aroma.cn , aroma.core , calmate Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package DNAcopy_1.84.0.tar.gz Windows Binary (x86_64) DNAcopy_1.84.0.zip macOS Binary (x86_64) DNAcopy_1.84.0.tgz macOS Binary (arm64) DNAcopy_1.84.0.tgz Source Repository git clone https://git.bioconductor.org/packages/DNAcopy Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DNAcopy Bioc Package Browser https://code.bioconductor.org/browse/DNAcopy/ Package Short Url https://bioconductor.org/packages/DNAcopy/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-dnacopy --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-dnacopy 1.44.0 r3.2.2_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.44.0-r3.2.2_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.44.0
+build       : r3.2.2_0
+build number: 0
+size        : 175 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.44.0-r3.2.2_0.tar.bz2
+md5         : c89dadade5cc3f2bc78daedc27015c89
+dependencies: 
+  - r 3.2.2*
+
+
+bioconductor-dnacopy 1.46.0 r3.3.1_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.46.0-r3.3.1_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.46.0
+build       : r3.3.1_0
+build number: 0
+size        : 178 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.3.1_0.tar.bz2
+md5         : fcf23d637d5d3045e73093bc0207390f
+dependencies: 
+  - r 3.3.1*
+
+
+bioconductor-dnacopy 1.46.0 r3.3.2_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.46.0-r3.3.2_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.46.0
+build       : r3.3.2_0
+build number: 0
+size        : 180 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.3.2_0.tar.bz2
+md5         : 43b4b704d1bf3704fce9fe7cd63508c0
+dependencies: 
+  - r-base 3.3.2*
+
+
+bioconductor-dnacopy 1.46.0 r3.4.1_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.46.0-r3.4.1_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.46.0
+build       : r3.4.1_0
+build number: 0
+size        : 183 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.46.0-r3.4.1_0.tar.bz2
+md5         : 2c540a9d895e43f2f2c23e9f8c9dc4ec
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-dnacopy 1.48.0 r3.3.2_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.48.0-r3.3.2_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.48.0
+build       : r3.3.2_0
+build number: 0
+size        : 183 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r3.3.2_0.tar.bz2
+md5         : 9c9300776d181451a107dc710b5ef9bf
+dependencies: 
+  - libgcc
+  - r-base 3.3.2*
+
+
+bioconductor-dnacopy 1.48.0 r3.4.1_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.48.0-r3.4.1_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.48.0
+build       : r3.4.1_0
+build number: 0
+size        : 183 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r3.4.1_0.tar.bz2
+md5         : a2b98c226bc26c0daab0421d0212bd7e
+dependencies: 
+  - libgcc
+  - r-base 3.4.1*
+
+
+bioconductor-dnacopy 1.48.0 r341h470a237_1
+------------------------------------------
+file name   : bioconductor-dnacopy-1.48.0-r341h470a237_1.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.48.0
+build       : r341h470a237_1
+build number: 1
+size        : 182 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r341h470a237_1.tar.bz2
+md5         : 83ee6a2ecf88a8216bd242b71ac3e924
+timestamp   : 2018-10-11 09:55:40 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-dnacopy 1.48.0 r351h470a237_1
+------------------------------------------
+file name   : bioconductor-dnacopy-1.48.0-r351h470a237_1.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.48.0
+build       : r351h470a237_1
+build number: 1
+size        : 225 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.48.0-r351h470a237_1.tar.bz2
+md5         : f53a5bf91768331b16922d593b50e4df
+timestamp   : 2018-10-11 09:56:35 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-dnacopy 1.50.1 r3.4.1_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.50.1-r3.4.1_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.50.1
+build       : r3.4.1_0
+build number: 0
+size        : 396 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.50.1-r3.4.1_0.tar.bz2
+md5         : ecba8e6b731ad22d6d36ec29c4fd8d2b
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-dnacopy 1.52.0 r3.4.1_0
+------------------------------------
+file name   : bioconductor-dnacopy-1.52.0-r3.4.1_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.52.0
+build       : r3.4.1_0
+build number: 0
+size        : 396 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.52.0-r3.4.1_0.tar.bz2
+md5         : 14aff29f14d9227e877df99023314174
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-dnacopy 1.54.0 r341ha44fe06_0
+------------------------------------------
+file name   : bioconductor-dnacopy-1.54.0-r341ha44fe06_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.54.0
+build       : r341ha44fe06_0
+build number: 0
+size        : 395 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.54.0-r341ha44fe06_0.tar.bz2
+md5         : 283a6f3d42120809c51ebb1139a345a9
+timestamp   : 2018-10-11 10:05:25 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - libgfortran >=3.0
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-dnacopy 1.54.0 r351ha44fe06_0
+------------------------------------------
+file name   : bioconductor-dnacopy-1.54.0-r351ha44fe06_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.54.0
+build       : r351ha44fe06_0
+build number: 0
+size        : 437 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.54.0-r351ha44fe06_0.tar.bz2
+md5         : c16d47cdd139f12aaae8322c5188c8ed
+timestamp   : 2018-10-11 10:06:15 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - libgfortran >=3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-dnacopy 1.56.0 r351h9ac9557_0
+------------------------------------------
+file name   : bioconductor-dnacopy-1.56.0-r351h9ac9557_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.56.0
+build       : r351h9ac9557_0
+build number: 0
+size        : 435 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.56.0-r351h9ac9557_0.tar.bz2
+md5         : 6c1c85cb39f84b924e05fe95782446f0
+timestamp   : 2018-12-10 10:45:10 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.5.1,<3.5.2.0a0
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+bioconductor-dnacopy 1.58.0 r351h9ac9557_0
+------------------------------------------
+file name   : bioconductor-dnacopy-1.58.0-r351h9ac9557_0.tar.bz2
+name        : bioconductor-dnacopy
+version     : 1.58.0
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+build number: 0
+size        : 435 KB
+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.58.0-r351h9ac9557_0.tar.bz2
+md5         : 2cf20df40125590e48a7cb6aa5580683
+timestamp   : 2019-05-09 12:24:35 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.5.1,<3.5.2.0a0
+
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+bioconductor-dnacopy 1.58.0 r36h6e990d7_1
+-----------------------------------------
+file name   : bioconductor-dnacopy-1.58.0-r36h6e990d7_1.tar.bz2
+name        : bioconductor-dnacopy
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+build number: 1
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+license     : GPL (>= 2)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-dnacopy-1.58.0-r36h6e990d7_1.tar.bz2
+md5         : 135914b4ecea2116a53c3b1c6c094159
+timestamp   : 2019-07-21 14:07:55 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-dnacopy 1.58.0 r36h6e990d7_2
+-----------------------------------------
+file name   : bioconductor-dnacopy-1.58.0-r36h6e990d7_2.tar.bz2
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+license     : GPL (>= 2)
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+md5         : 61efc8fce58bdc90469a75b9701c0e91
+timestamp   : 2019-10-29 10:42:16 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.6,<3.7.0a0
+
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+-----------------------------------------
+file name   : bioconductor-dnacopy-1.60.0-r36h6e990d7_0.tar.bz2
+name        : bioconductor-dnacopy
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+license     : GPL (>= 2)
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+md5         : e29072e0c925a82b32902a19df22420e
+timestamp   : 2019-11-01 09:34:18 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-dnacopy 1.62.0 r40h323e27b_0
+-----------------------------------------
+file name   : bioconductor-dnacopy-1.62.0-r40h323e27b_0.tar.bz2
+name        : bioconductor-dnacopy
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+  - libgcc-ng >=7.3.0
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+  - liblapack >=3.8.0,<3.9.0a0
+  - r-base >=4.0,<4.1.0a0
+
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+-----------------------------------------
+file name   : bioconductor-dnacopy-1.64.0-r40h323e27b_0.tar.bz2
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+-----------------------------------------
+file name   : bioconductor-dnacopy-1.64.0-r40hacda110_1.tar.bz2
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+timestamp   : 2021-03-26 03:44:18 UTC
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+
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+-----------------------------------------
+file name   : bioconductor-dnacopy-1.66.0-r41hacda110_0.tar.bz2
+name        : bioconductor-dnacopy
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+timestamp   : 2021

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-ebseq.manual_bundle.txt

@@ -0,0 +1,444 @@
+# Tool: bioconductor-ebseq
+software_name: bioconductor-ebseq
+tier: T1
+domain: t1_backfill_overall
+downloads: 124439
+summary: An R package for gene and isoform differential expression analysis of RNA-seq data
+description: Differential Expression analysis at both gene and isoform level using RNA-seq data
+dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh <=1.87.0-1, r-blockmodeling, r-gplots, r-rcpp >=0.12.11, r-rcppeigen >=0.3.2.9.0, r-testthat
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/EBSeq.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/EBSeq.html
+Bioconductor - EBSeq Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages EBSeq EBSeq This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see EBSeq . An R package for gene and isoform differential expression analysis of RNA-seq data DOI: 10.18129/B9.bioc.EBSeq Bioconductor version: 3.22 Differential Expression analysis at both gene and isoform level using RNA-seq data Author: Xiuyu Ma [cre, aut], Ning Leng [aut], Christina Kendziorski [ctb], Michael A. Newton [ctb] Maintainer: Xiuyu Ma &#x3c;&#x77;&#x61;&#x74;&#x73;&#x6f;&#x6e;&#x66;&#x6f;&#x72;&#x66;&#x75;&#x6e;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("EBSeq") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("EBSeq") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("EBSeq") EBSeq Vignette PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , ImmunoOncology , MultipleComparison , RNASeq , Sequencing , Software , StatisticalMethod Version 2.8.0 In Bioconductor since BioC 2.13 (R-3.0) (12.5 years) License Artistic-2.0 Depends blockmodeling , gplots , testthat , R (>= 3.0.0) Imports Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0), BH ( System Requirements c++14 URL See More Suggests Linking To Rcpp , RcppEigen , BH Enhances Depends On Me Oscope Imports Me BatchQC , broadSeq , DEsubs , scDD Suggests Me compcodeR Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package EBSeq_2.8.0.tar.gz Windows Binary (x86_64) EBSeq_2.8.0.zip macOS Binary (x86_64) EBSeq_2.8.0.tgz macOS Binary (arm64) EBSeq_2.8.0.tgz Source Repository git clone https://git.bioconductor.org/packages/EBSeq Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/EBSeq Bioc Package Browser https://code.bioconductor.org/browse/EBSeq/ Package Short Url https://bioconductor.org/packages/EBSeq/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-ebseq --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-ebseq 1.12.0 0
+---------------------------
+file name   : bioconductor-ebseq-1.12.0-0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.12.0
+build       : 0
+build number: 0
+size        : 1004 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.12.0-0.tar.bz2
+md5         : d2d052e244d776d3c915058e8bc6fb0b
+dependencies: 
+  - r >=3.0.0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.14.0 r3.3.1_0
+----------------------------------
+file name   : bioconductor-ebseq-1.14.0-r3.3.1_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.14.0
+build       : r3.3.1_0
+build number: 0
+size        : 180 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.1_0.tar.bz2
+md5         : b35ea585a62637d678e7b324fa6bf668
+dependencies: 
+  - r 3.3.1*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.14.0 r3.3.1_1
+----------------------------------
+file name   : bioconductor-ebseq-1.14.0-r3.3.1_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.14.0
+build       : r3.3.1_1
+build number: 1
+size        : 180 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.1_1.tar.bz2
+md5         : 61c12f97a1652baf1f53159c5344abf8
+dependencies: 
+  - r-base 3.3.1*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.14.0 r3.3.2_1
+----------------------------------
+file name   : bioconductor-ebseq-1.14.0-r3.3.2_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.14.0
+build       : r3.3.2_1
+build number: 1
+size        : 183 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.3.2_1.tar.bz2
+md5         : 6370cfe2ed729d0f27337c59f44ad573
+dependencies: 
+  - r-base 3.3.2*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.14.0 r3.4.1_1
+----------------------------------
+file name   : bioconductor-ebseq-1.14.0-r3.4.1_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.14.0
+build       : r3.4.1_1
+build number: 1
+size        : 185 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.14.0-r3.4.1_1.tar.bz2
+md5         : 1228a17412e9c4aad4cc2661ef8c294f
+dependencies: 
+  - r-base 3.4.1*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.16.0 r3.4.1_0
+----------------------------------
+file name   : bioconductor-ebseq-1.16.0-r3.4.1_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.16.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.0 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.16.0-r3.4.1_0.tar.bz2
+md5         : 77b77081b58180c6f722c0fffaffb63e
+dependencies: 
+  - r-base 3.4.1*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.18.0 r3.4.1_0
+----------------------------------
+file name   : bioconductor-ebseq-1.18.0-r3.4.1_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.18.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.0 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.18.0-r3.4.1_0.tar.bz2
+md5         : df757d5743a7cbad81dca429510083fd
+dependencies: 
+  - r-base 3.4.1*
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.20.0 r341_0
+--------------------------------
+file name   : bioconductor-ebseq-1.20.0-r341_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.20.0
+build       : r341_0
+build number: 0
+size        : 1.0 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.20.0-r341_0.tar.bz2
+md5         : cfd9a2b5e9f16734bbb5ec76aec9e23a
+timestamp   : 2018-10-12 08:32:21 UTC
+dependencies: 
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.20.0 r351_0
+--------------------------------
+file name   : bioconductor-ebseq-1.20.0-r351_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.20.0
+build       : r351_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-ebseq-1.20.0-r351_0.tar.bz2
+md5         : 47a3ce99ebea3771b1a6e41fd39b0da3
+timestamp   : 2018-10-12 08:33:41 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.22.0 r351_0
+--------------------------------
+file name   : bioconductor-ebseq-1.22.0-r351_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.22.0
+build       : r351_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.22.0-r351_0.tar.bz2
+md5         : 34f040f737a8dcbd34b293224fb91828
+timestamp   : 2018-12-10 10:10:17 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.22.1 r351_0
+--------------------------------
+file name   : bioconductor-ebseq-1.22.1-r351_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.22.1
+build       : r351_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.22.1-r351_0.tar.bz2
+md5         : e98639d1a17bf839f642c620612fdc5b
+timestamp   : 2019-04-24 02:57:43 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.24.0 r351_0
+--------------------------------
+file name   : bioconductor-ebseq-1.24.0-r351_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.24.0
+build       : r351_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.24.0-r351_0.tar.bz2
+md5         : 08c32c78a3ef7983373fb30ec852c345
+timestamp   : 2019-05-09 10:46:15 UTC
+dependencies: 
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.24.0 r36_1
+-------------------------------
+file name   : bioconductor-ebseq-1.24.0-r36_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.24.0
+build       : r36_1
+build number: 1
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.24.0-r36_1.tar.bz2
+md5         : 0207830b16ba250579cdf644f938b248
+timestamp   : 2019-07-22 04:22:22 UTC
+dependencies: 
+  - r-base >=3.6,<3.7.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.26.0 r36_0
+-------------------------------
+file name   : bioconductor-ebseq-1.26.0-r36_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.26.0
+build       : r36_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.26.0-r36_0.tar.bz2
+md5         : ccdb12b6bd451e7de31e263747fd28a6
+timestamp   : 2019-11-01 16:21:20 UTC
+dependencies: 
+  - r-base >=3.6,<3.7.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.28.0 r40_0
+-------------------------------
+file name   : bioconductor-ebseq-1.28.0-r40_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.28.0
+build       : r40_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.28.0-r40_0.tar.bz2
+md5         : 4263da5a0baa480c638712840f199b3b
+timestamp   : 2020-05-09 14:20:58 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.30.0 r40_0
+-------------------------------
+file name   : bioconductor-ebseq-1.30.0-r40_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.30.0
+build       : r40_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.30.0-r40_0.tar.bz2
+md5         : aa29dbd2682704b8434e5fc98a100c85
+timestamp   : 2020-10-29 10:57:09 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.30.0 r40hdfd78af_1
+---------------------------------------
+file name   : bioconductor-ebseq-1.30.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.30.0
+build       : r40hdfd78af_1
+build number: 1
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.30.0-r40hdfd78af_1.tar.bz2
+md5         : c365c43e61501f9834f915d18f541161
+timestamp   : 2021-03-24 23:42:00 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.32.0 r41hdfd78af_0
+---------------------------------------
+file name   : bioconductor-ebseq-1.32.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.32.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.32.0-r41hdfd78af_0.tar.bz2
+md5         : f2f4b8821cda3085b5ba1fd32426528e
+timestamp   : 2021-05-31 07:14:29 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.34.0 r41hdfd78af_0
+---------------------------------------
+file name   : bioconductor-ebseq-1.34.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.34.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.34.0-r41hdfd78af_0.tar.bz2
+md5         : 6bf7169eaf8067a869dfa28bba8d09ae
+timestamp   : 2021-11-02 10:01:36 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.38.0 r42hdfd78af_0
+---------------------------------------
+file name   : bioconductor-ebseq-1.38.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.38.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.38.0-r42hdfd78af_0.tar.bz2
+md5         : 837915318ed184ff8209a6643ae4c2b2
+timestamp   : 2022-11-03 17:13:05 UTC
+dependencies: 
+  - r-base >=4.2,<4.3.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 1.40.0 r43hdfd78af_0
+---------------------------------------
+file name   : bioconductor-ebseq-1.40.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-ebseq
+version     : 1.40.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-ebseq-1.40.0-r43hdfd78af_0.tar.bz2
+md5         : 92e3f21a157bfb4e4d2c1da0e823c308
+timestamp   : 2023-07-07 07:13:46 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+  - r-blockmodeling
+  - r-gplots
+  - r-testthat
+
+
+bioconductor-ebseq 2.0.0 r43hf17093f_1
+--------------------------------------
+file name   : bioconductor-ebseq-2.0.0-r43hf17093f_1.tar.bz2
+name        : bioconductor-ebseq
+version     : 2.0.0
+build

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-fgsea.manual_bundle.txt

@@ -0,0 +1,436 @@
+# Tool: bioconductor-fgsea
+software_name: bioconductor-fgsea
+tier: T1
+domain: t1_backfill_overall
+downloads: 142910
+summary: Fast Gene Set Enrichment Analysis
+description: The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-biocparallel >=1.44.0,<1.45.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh, r-cowplot, r-data.table, r-fastmatch, r-ggplot2 >=2.2.0, r-matrix, r-rcpp, r-scales
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: http://bioconductor.org/packages/3.5/bioc/html/fgsea.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### http://bioconductor.org/packages/3.5/bioc/html/fgsea.html
+Bioconductor - fgsea Home Bioconductor 3.5 Software Packages fgsea To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("fgsea") In most cases, you don't need to download the package archive at all. fgsea DOI: 10.18129/B9.bioc.fgsea &nbsp; &nbsp; Fast Gene Set Enrichment Analysis Bioconductor version: Release (3.5) The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. Author: Alexey Sergushichev [aut, cre] Maintainer: Alexey Sergushichev &#x3c;&#x61;&#x6c;&#x73;&#x65;&#x72;&#x67;&#x62;&#x6f;&#x78;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("fgsea") ): Installation To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("fgsea") Documentation HTML R Script Using fgsea package PDF &nbsp; Reference Manual Text &nbsp; NEWS Details biocViews DifferentialExpression , GeneExpression , GeneSetEnrichment , Pathways , Software Version 1.2.1 In Bioconductor since BioC 3.4 (R-3.3) (1 year) License MIT + file LICENCE Depends R (>= 3.3), Rcpp Imports data.table , BiocParallel , stats, ggplot2 (>= 2.2.0), gridExtra , grid, fastmatch LinkingTo Rcpp Suggests testthat , knitr , rmarkdown , reactome.db , AnnotationDbi , parallel SystemRequirements C++11 Enhances URL https://github.com/ctlab/fgsea/ BugReports https://github.com/ctlab/fgsea/issues Depends On Me PPInfer Imports Me DOSE , piano Suggests Me Pi Build Report &nbsp; Package Archives Follow Installation instructions to use this package in your R session. Source Package fgsea_1.2.1.tar.gz Windows Binary fgsea_1.2.1.zip (32- &amp; 64-bit) Mac OS X 10.11 (El Capitan) fgsea_1.2.1.tgz Source Repository git clone https://git.bioconductor.org/packages/fgsea Package Short Url http://bioconductor.org/packages/fgsea/ Package Downloads Report Download Stats Documentation &raquo; Bioconductor Package vignettes and manuals. Workflows for learning and use. Course and conference material. Videos . Community resources and tutorials . R / CRAN packages and documentation Support &raquo; Please read the posting guide . Post questions about Bioconductor to one of the following locations: Support site - for questions about Bioconductor packages Bioc-devel mailing list - for package developers Contact us: support.bioconductor.org Copyright &copy; 2003 - 2017, Bioconductor Home Install Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Help Workflows Package Vignettes FAQ Support Using R Courses Publications Cloud AMI Community Resources Developers Package Guidelines Package Submission Release Schedule Source Control About Advisory Board Annual Reports Core Team Mirrors Related Projects &nbsp; Search: Home Install Help Developers About
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-fgsea --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-fgsea 1.2.1 0
+--------------------------
+file name   : bioconductor-fgsea-1.2.1-0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.2.1
+build       : 0
+build number: 0
+size        : 799 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.2.1-0.tar.bz2
+md5         : 76a3149643da0890f8af84d26e34db54
+dependencies: 
+  - bioconductor-biocparallel
+  - r-base >=3.3,<3.4
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-rcpp
+
+
+bioconductor-fgsea 1.4.0 r3.4.1_0
+---------------------------------
+file name   : bioconductor-fgsea-1.4.0-r3.4.1_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.4.0
+build       : r3.4.1_0
+build number: 0
+size        : 801 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.4.0-r3.4.1_0.tar.bz2
+md5         : 2caa4ea03fea70a129339e676ea0340c
+dependencies: 
+  - bioconductor-biocparallel
+  - r-base 3.4.1*
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-rcpp
+
+
+bioconductor-fgsea 1.6.0 r341hfc679d8_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.6.0-r341hfc679d8_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.6.0
+build       : r341hfc679d8_0
+build number: 0
+size        : 956 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.6.0-r341hfc679d8_0.tar.bz2
+md5         : dca739e172bb60632bd30ef008e6c20a
+timestamp   : 2018-10-12 01:35:30 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.14.2,<1.16.0
+  - libgcc-ng >=4.9
+  - libstdcxx-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.6.0 r351hfc679d8_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.6.0-r351hfc679d8_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.6.0
+build       : r351hfc679d8_0
+build number: 0
+size        : 976 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.6.0-r351hfc679d8_0.tar.bz2
+md5         : 3632ee167120ac604aba00641d325317
+timestamp   : 2018-10-12 01:33:44 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.14.2,<1.16.0
+  - libgcc-ng >=4.9
+  - libstdcxx-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.8.0 r351hf484d3e_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.8.0-r351hf484d3e_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.8.0
+build       : r351hf484d3e_0
+build number: 0
+size        : 895 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.8.0-r351hf484d3e_0.tar.bz2
+md5         : 54b11a7a868c968e98e7b18d3f282b2a
+timestamp   : 2018-12-12 01:58:42 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.16.0,<1.17.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.10.0 r351hf484d3e_0
+----------------------------------------
+file name   : bioconductor-fgsea-1.10.0-r351hf484d3e_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.10.0
+build       : r351hf484d3e_0
+build number: 0
+size        : 986 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.10.0-r351hf484d3e_0.tar.bz2
+md5         : f458552f46f024cac576e66a3e3c1054
+timestamp   : 2019-05-09 19:02:12 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.18.0,<1.19.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.10.0 r36he1b5a44_1
+---------------------------------------
+file name   : bioconductor-fgsea-1.10.0-r36he1b5a44_1.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.10.0
+build       : r36he1b5a44_1
+build number: 1
+size        : 962 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.10.0-r36he1b5a44_1.tar.bz2
+md5         : 6c6bdb7144c32dcef52538a10ad0afdb
+timestamp   : 2019-07-22 01:44:47 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.18.0,<1.19.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.12.0 r36he1b5a44_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.12.0-r36he1b5a44_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.12.0
+build       : r36he1b5a44_0
+build number: 0
+size        : 1002 KB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.12.0-r36he1b5a44_0.tar.bz2
+md5         : c5d7fcab3fa94013db30e27b7bcebf3a
+timestamp   : 2019-11-02 13:24:50 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.20.0,<1.21.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.14.0 r40h5f743cb_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.14.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.14.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.14.0-r40h5f743cb_0.tar.bz2
+md5         : b5825068488351ed574199462544b022
+timestamp   : 2020-05-10 07:14:10 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.22.0,<1.23.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.16.0 r40h399db7b_1
+---------------------------------------
+file name   : bioconductor-fgsea-1.16.0-r40h399db7b_1.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.16.0
+build       : r40h399db7b_1
+build number: 1
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.16.0-r40h399db7b_1.tar.bz2
+md5         : 204726c5251afc70c75c7e24194dd0e0
+timestamp   : 2021-03-27 23:03:15 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.16.0 r40h5f743cb_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.16.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.16.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.16.0-r40h5f743cb_0.tar.bz2
+md5         : 87eb98f3aab39051bef018b6b3387fe7
+timestamp   : 2020-10-29 21:58:15 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.24.0,<1.25.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=7.5.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.18.0 r41h399db7b_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.18.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.18.0
+build       : r41h399db7b_0
+build number: 0
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.18.0-r41h399db7b_0.tar.bz2
+md5         : 5a71a6151ebf62d77aa1d053e8d0c233
+timestamp   : 2021-05-31 09:34:30 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.26.0,<1.27.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.20.0 r41h399db7b_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.20.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.20.0
+build       : r41h399db7b_0
+build number: 0
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41h399db7b_0.tar.bz2
+md5         : d753665dd092dde5675f62c05e3fe6a9
+timestamp   : 2021-11-02 14:54:14 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.4.0
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.20.0 r41h619a076_1
+---------------------------------------
+file name   : bioconductor-fgsea-1.20.0-r41h619a076_1.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.20.0
+build       : r41h619a076_1
+build number: 1
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41h619a076_1.tar.bz2
+md5         : 79aa657b52180aabfea2e53e38d93ac5
+timestamp   : 2022-02-24 13:05:37 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=10.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.20.0 r41hc247a5b_2
+---------------------------------------
+file name   : bioconductor-fgsea-1.20.0-r41hc247a5b_2.tar.bz2
+name        : bioconductor-fgsea
+version     : 1.20.0
+build       : r41hc247a5b_2
+build number: 2
+size        : 1.4 MB
+license     : MIT + file LICENCE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-fgsea-1.20.0-r41hc247a5b_2.tar.bz2
+md5         : 8bdc49d145bf8ad41ada4c6ecdfade27
+timestamp   : 2022-09-15 09:17:26 UTC
+dependencies: 
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+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+  - r-data.table
+  - r-fastmatch
+  - r-ggplot2 >=2.2.0
+  - r-gridextra
+  - r-matrix
+  - r-rcpp
+
+
+bioconductor-fgsea 1.24.0 r42hc247a5b_0
+---------------------------------------
+file name   : bioconductor-fgsea-1.24.0-r42hc247a5b_0.tar.bz2
+name        : bioconductor-fgsea
+version     :

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-geneplotter.manual_bundle.txt

@@ -0,0 +1,411 @@
+# Tool: bioconductor-geneplotter
+software_name: bioconductor-geneplotter
+tier: T1
+domain: t1_backfill_overall
+downloads: 462579
+summary: Graphics related functions for Bioconductor
+description: Functions for plotting genomic data
+dependencies: bioconductor-annotate >=1.88.0,<1.89.0, bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-biobase >=2.70.0,<2.71.0, bioconductor-biocgenerics >=0.56.0,<0.57.0, r-base >=4.5,<4.6.0a0, r-lattice, r-rcolorbrewer
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/geneplotter.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/geneplotter.html
+Bioconductor - geneplotter Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages geneplotter geneplotter This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see geneplotter . Graphics related functions for Bioconductor DOI: 10.18129/B9.bioc.geneplotter Bioconductor version: 3.22 Functions for plotting genomic data Author: Robert Gentleman [aut], Rohit Satyam [ctb] (Converted geneplotter vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("geneplotter") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("geneplotter") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("geneplotter") How to Assemble a chromLocation Object HTML R Script Visualization of Microarray Data PDF R Script Reference Manual PDF README Text NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Software , Visualization Version 1.88.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (&gt; 21 years) License Artistic-2.0 Depends R (>= 2.10), methods, Biobase , BiocGenerics , lattice , annotate Imports AnnotationDbi , graphics, grDevices, grid, RColorBrewer , stats, utils System Requirements URL See More Suggests Rgraphviz , fibroEset , hgu95av2.db , hu6800.db , hgu133a.db , BiocStyle , knitr Linking To Enhances Depends On Me HD2013SGI , Hiiragi2013 , maEndToEnd Imports Me biocGraph , DEXSeq , MethylSeekR Suggests Me biocGraph , Category , EnrichmentBrowser , GOstats , Single.mTEC.Transcriptomes Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package geneplotter_1.88.0.tar.gz Windows Binary (x86_64) geneplotter_1.88.0.zip macOS Binary (x86_64) geneplotter_1.88.0.tgz macOS Binary (arm64) geneplotter_1.88.0.tgz Source Repository git clone https://git.bioconductor.org/packages/geneplotter Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/geneplotter Bioc Package Browser https://code.bioconductor.org/browse/geneplotter/ Package Short Url https://bioconductor.org/packages/geneplotter/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-geneplotter --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-geneplotter 1.46.0 0
+---------------------------------
+file name   : bioconductor-geneplotter-1.46.0-0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.46.0
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.46.0-0.tar.bz2
+md5         : 92d36ae78e56eda61c92c104fd32f823
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r >=2.10
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.48.0 0
+---------------------------------
+file name   : bioconductor-geneplotter-1.48.0-0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.48.0
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.48.0-0.tar.bz2
+md5         : 2a2d0e29972a95dbb1ca381385c7c8f3
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r >=2.10
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.50.0 r3.3.1_0
+----------------------------------------
+file name   : bioconductor-geneplotter-1.50.0-r3.3.1_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.50.0
+build       : r3.3.1_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.3.1_0.tar.bz2
+md5         : e2a81595f867e62064c4fdec03939026
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r 3.3.1*
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.50.0 r3.3.2_0
+----------------------------------------
+file name   : bioconductor-geneplotter-1.50.0-r3.3.2_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.50.0
+build       : r3.3.2_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.3.2_0.tar.bz2
+md5         : ab52644b69cf2ddf3d8bf36fadd3118f
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r-base 3.3.2*
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.50.0 r3.4.1_0
+----------------------------------------
+file name   : bioconductor-geneplotter-1.50.0-r3.4.1_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.50.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.1 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.50.0-r3.4.1_0.tar.bz2
+md5         : 0e7dc22113275c6f8a21357f351c6ad2
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.54.0 r3.4.1_0
+----------------------------------------
+file name   : bioconductor-geneplotter-1.54.0-r3.4.1_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.54.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.54.0-r3.4.1_0.tar.bz2
+md5         : 0580cfb140cdf9332d5f5d9afffba4f2
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.56.0 r3.4.1_0
+----------------------------------------
+file name   : bioconductor-geneplotter-1.56.0-r3.4.1_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.56.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.56.0-r3.4.1_0.tar.bz2
+md5         : f5ba800c8c0cd38fd55dae3fe3084f9c
+dependencies: 
+  - bioconductor-annotate
+  - bioconductor-annotationdbi
+  - bioconductor-biobase
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.58.0 r341_0
+--------------------------------------
+file name   : bioconductor-geneplotter-1.58.0-r341_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.58.0
+build       : r341_0
+build number: 0
+size        : 1.4 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.58.0-r341_0.tar.bz2
+md5         : f543e04732078f5453d27f8d93854a53
+timestamp   : 2018-10-25 07:42:38 UTC
+dependencies: 
+  - bioconductor-annotate >=1.58.0,<1.60.0
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - bioconductor-biobase >=2.40.0,<2.42.0
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.58.0 r351_0
+--------------------------------------
+file name   : bioconductor-geneplotter-1.58.0-r351_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.58.0
+build       : r351_0
+build number: 0
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-geneplotter-1.58.0-r351_0.tar.bz2
+md5         : c06ea26c34402a0f2d7e09a24c990128
+timestamp   : 2018-10-25 07:44:22 UTC
+dependencies: 
+  - bioconductor-annotate >=1.58.0,<1.60.0
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - bioconductor-biobase >=2.40.0,<2.42.0
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.60.0 r351_0
+--------------------------------------
+file name   : bioconductor-geneplotter-1.60.0-r351_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.60.0
+build       : r351_0
+build number: 0
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.60.0-r351_0.tar.bz2
+md5         : 89a31d794ef42cfbd3543eb48a64c00b
+timestamp   : 2019-01-01 11:16:48 UTC
+dependencies: 
+  - bioconductor-annotate >=1.60.0,<1.61.0
+  - bioconductor-annotationdbi >=1.44.0,<1.45.0
+  - bioconductor-biobase >=2.42.0,<2.43.0
+  - bioconductor-biocgenerics >=0.28.0,<0.29.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.62.0 r36_1
+-------------------------------------
+file name   : bioconductor-geneplotter-1.62.0-r36_1.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.62.0
+build       : r36_1
+build number: 1
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+md5         : 7322ff8d509de80f8d5dbb904c6d7238
+timestamp   : 2019-08-06 13:41:04 UTC
+dependencies: 
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+  - r-base >=3.6,<3.7.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.64.0 r36_0
+-------------------------------------
+file name   : bioconductor-geneplotter-1.64.0-r36_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.64.0
+build       : r36_0
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.64.0-r36_0.tar.bz2
+md5         : 2008ae86507430a91e824bd01e3c7d1c
+timestamp   : 2019-11-03 21:52:32 UTC
+dependencies: 
+  - bioconductor-annotate >=1.64.0,<1.65.0
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+  - r-base >=3.6,<3.7.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.66.0 r40_0
+-------------------------------------
+file name   : bioconductor-geneplotter-1.66.0-r40_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.66.0
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+build number: 0
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.66.0-r40_0.tar.bz2
+md5         : 1da247091a0ef5b5b29bc011aec551f2
+timestamp   : 2020-05-11 06:47:15 UTC
+dependencies: 
+  - bioconductor-annotate >=1.66.0,<1.67.0
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+  - r-base >=4.0,<4.1.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.68.0 r40_0
+-------------------------------------
+file name   : bioconductor-geneplotter-1.68.0-r40_0.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.68.0
+build       : r40_0
+build number: 0
+size        : 1.5 MB
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.68.0-r40_0.tar.bz2
+md5         : 757e5398600856f144749fdeb2b0d046
+timestamp   : 2020-10-30 14:51:03 UTC
+dependencies: 
+  - bioconductor-annotate >=1.68.0,<1.69.0
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
+  - bioconductor-biobase >=2.50.0,<2.51.0
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+  - r-base >=4.0,<4.1.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.68.0 r40hdfd78af_1
+---------------------------------------------
+file name   : bioconductor-geneplotter-1.68.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-geneplotter
+version     : 1.68.0
+build       : r40hdfd78af_1
+build number: 1
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-geneplotter-1.68.0-r40hdfd78af_1.tar.bz2
+md5         : fca7f5dcd41558d3bfbc508bec75019b
+timestamp   : 2021-03-30 07:10:15 UTC
+dependencies: 
+  - bioconductor-annotate >=1.68.0,<1.69.0
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
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+  - r-base >=4.0,<4.1.0a0
+  - r-lattice
+  - r-rcolorbrewer
+
+
+bioconductor-geneplotter 1.70.0 r41hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-geneplotter-1.70.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-geneplotter
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+md5         : 85fa97ce70a3df599f6b583e09fcfb94
+timestamp   : 2021-06-01 21:53:07 UTC
+dependencies: 
+  - bioconductor-annotate >=1.70.0,<1.71.0
+  - bioconductor-annotationdbi >=1.54.0,<1.55.0
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+  - r-base >=4.1,<4.2.0a0
+  - r-lattice
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+bioconductor-geneplotter 1.72.0 r41hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-geneplotter-1.72.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-geneplotter
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+md5         : 32c0e22a0095ad9b592a6bf7e16a835a
+timestamp   : 2021-11-06 01:31:33 UTC
+depend

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-glmgampoi.manual_bundle.txt

@@ -0,0 +1,363 @@
+# Tool: bioconductor-glmgampoi
+software_name: bioconductor-glmgampoi
+tier: T1
+domain: t1_backfill_overall
+downloads: 265321
+summary: Fit a Gamma-Poisson Generalized Linear Model
+description: Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.
+dependencies: bioconductor-assorthead >=1.4.0,<1.5.0, bioconductor-assorthead >=1.4.0,<1.5.0a0, bioconductor-beachmat >=2.26.0,<2.27.0, bioconductor-beachmat >=2.26.0,<2.27.0a0, bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-delayedarray >=0.36.0,<0.37.0a0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0, bioconductor-delayedmatrixstats >=1.32.0,<1.33.0a0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-hdf5array >=1.38.0,<1.39.0a0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0a0, bioconductor-sparsearray >=1.10.0,<1.11.0, bioconductor-sparsearray >=1.10.8,<1.11.0a0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix, r-matrixstats, r-rcpp, r-rcpparmadillo, r-rlang, r-vctrs
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.11/bioc/html/glmGamPoi.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.11/bioc/html/glmGamPoi.html
+Bioconductor - glmGamPoi About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages glmGamPoi glmGamPoi This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see glmGamPoi . Fit a Gamma-Poisson Generalized Linear Model DOI: 10.18129/B9.bioc.glmGamPoi Bioconductor version: 3.11 Fit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments. Author: Constantin Ahlmann-Eltze [aut, cre] , Michael Love [ctb] Maintainer: Constantin Ahlmann-Eltze &#x3c;&#x61;&#x72;&#x74;&#x6a;&#x6f;&#x6d;&#x33;&#x31;&#x34;&#x31;&#x35;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6f;&#x6f;&#x67;&#x6c;&#x65;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("glmGamPoi") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("glmGamPoi") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("glmGamPoi") glmGamPoi Quickstart HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews RNASeq , Regression , SingleCell , Software Version 1.0.0 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License GPL-3 Depends Imports Rcpp, pracma, DelayedMatrixStats , DelayedArray , HDF5Array , SummarizedExperiment , methods, stats, utils System Requirements C++11 URL https://github.com/const-ae/glmGamPoi Bug Reports https://github.com/const-ae/glmGamPoi/issues See More Suggests testthat (>= 2.1.0), zoo, DESeq2 , edgeR , beachmat , MASS, statmod, ggplot2, bench, BiocParallel , knitr, rmarkdown, BiocStyle , TENxPBMCData Linking To Rcpp, RcppArmadillo, beachmat (>= 2.0.0) Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package glmGamPoi_1.0.0.tar.gz Windows Binary glmGamPoi_1.0.0.zip (32- &amp; 64-bit) macOS 10.13 (High Sierra) glmGamPoi_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/glmGamPoi Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/glmGamPoi Bioc Package Browser https://code.bioconductor.org/browse/glmGamPoi/ Package Short Url https://bioconductor.org/packages/glmGamPoi/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-glmgampoi --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-glmgampoi 1.0.0 r40h5f743cb_0
+------------------------------------------
+file name   : bioconductor-glmgampoi-1.0.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-glmgampoi
+version     : 1.0.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 668 KB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.0.0-r40h5f743cb_0.tar.bz2
+md5         : a093428ff266b994ce9e2cb43b7f870a
+timestamp   : 2020-05-11 04:07:26 UTC
+dependencies: 
+  - bioconductor-beachmat >=2.4.0,<2.5.0
+  - bioconductor-delayedarray >=0.14.0,<0.15.0
+  - bioconductor-delayedmatrixstats >=1.10.0,<1.11.0
+  - bioconductor-hdf5array >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.18.0,<1.19.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-pracma
+  - r-rcpp
+  - r-rcpparmadillo
+
+
+bioconductor-glmgampoi 1.2.0 r40h399db7b_1
+------------------------------------------
+file name   : bioconductor-glmgampoi-1.2.0-r40h399db7b_1.tar.bz2
+name        : bioconductor-glmgampoi
+version     : 1.2.0
+build       : r40h399db7b_1
+build number: 1
+size        : 771 KB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.2.0-r40h399db7b_1.tar.bz2
+md5         : 970fbfc553e6c0aebecaf0ca648b7150
+timestamp   : 2021-03-29 10:17:15 UTC
+dependencies: 
+  - bioconductor-beachmat >=2.6.0,<2.7.0
+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0
+  - bioconductor-hdf5array >=1.18.0,<1.19.0
+  - bioconductor-summarizedexperiment >=1.20.0,<1.21.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrixstats
+  - r-rcpp
+  - r-rcpparmadillo
+
+
+bioconductor-glmgampoi 1.2.0 r40h5f743cb_0
+------------------------------------------
+file name   : bioconductor-glmgampoi-1.2.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-glmgampoi
+version     : 1.2.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 762 KB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.2.0-r40h5f743cb_0.tar.bz2
+md5         : 6570b8cc1fd1d47c7cfebaf6f0e73256
+timestamp   : 2020-10-30 16:48:53 UTC
+dependencies: 
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+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-delayedmatrixstats >=1.12.0,<1.13.0
+  - bioconductor-hdf5array >=1.18.0,<1.19.0
+  - bioconductor-summarizedexperiment >=1.20.0,<1.21.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=7.5.0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrixstats
+  - r-rcpp
+  - r-rcpparmadillo
+
+
+bioconductor-glmgampoi 1.4.0 r41h399db7b_0
+------------------------------------------
+file name   : bioconductor-glmgampoi-1.4.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-glmgampoi
+version     : 1.4.0
+build       : r41h399db7b_0
+build number: 0
+size        : 1.2 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.4.0-r41h399db7b_0.tar.bz2
+md5         : 3250e1a8d47ff226c29bb268e595942a
+timestamp   : 2021-06-02 21:25:11 UTC
+dependencies: 
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+  - bioconductor-biocgenerics >=0.38.0,<0.39.0
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+  - bioconductor-delayedmatrixstats >=1.14.0,<1.15.0
+  - bioconductor-hdf5array >=1.20.0,<1.21.0
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+  - libblas >=3.8.0,<4.0a0
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+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrixstats
+  - r-rcpp
+  - r-rcpparmadillo
+
+
+bioconductor-glmgampoi 1.6.0 r41h399db7b_0
+------------------------------------------
+file name   : bioconductor-glmgampoi-1.6.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-glmgampoi
+version     : 1.6.0
+build       : r41h399db7b_0
+build number: 0
+size        : 1.2 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41h399db7b_0.tar.bz2
+md5         : 1c328106c0870c0df94455b62d7a8b68
+timestamp   : 2021-11-03 17:09:14 UTC
+dependencies: 
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+  - r-base >=4.1,<4.2.0a0
+  - r-matrixstats
+  - r-rcpp
+  - r-rcpparmadillo
+
+
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+------------------------------------------
+file name   : bioconductor-glmgampoi-1.6.0-r41h619a076_1.tar.bz2
+name        : bioconductor-glmgampoi
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+build       : r41h619a076_1
+build number: 1
+size        : 1.2 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41h619a076_1.tar.bz2
+md5         : e4ed4111be269626349a619b3d9b27f5
+timestamp   : 2022-02-27 11:47:04 UTC
+dependencies: 
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+  - r-base >=4.1,<4.2.0a0
+  - r-matrixstats
+  - r-rcpp
+  - r-rcpparmadillo
+
+
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+------------------------------------------
+file name   : bioconductor-glmgampoi-1.6.0-r41hc247a5b_2.tar.bz2
+name        : bioconductor-glmgampoi
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+build       : r41hc247a5b_2
+build number: 2
+size        : 1.2 MB
+license     : GPL-3
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.6.0-r41hc247a5b_2.tar.bz2
+md5         : aa1202e07d6dc79e6938f3a802660193
+timestamp   : 2022-09-23 15:08:05 UTC
+dependencies: 
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+  - r-base >=4.1,<4.2.0a0
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+
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+-------------------------------------------
+file name   : bioconductor-glmgampoi-1.10.0-r42hc247a5b_0.tar.bz2
+name        : bioconductor-glmgampoi
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+license     : GPL-3
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.10.0-r42hc247a5b_0.tar.bz2
+md5         : d3833c8f2be61c4664ea9cd3eb2dd88b
+timestamp   : 2022-11-06 11:20:32 UTC
+dependencies: 
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+
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+-------------------------------------------
+file name   : bioconductor-glmgampoi-1.10.0-r42hf17093f_1.tar.bz2
+name        : bioconductor-glmgampoi
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+md5         : 80fa24116aaba87ecc3fa456d77d6015
+timestamp   : 2023-05-28 09:29:08 UTC
+dependencies: 
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+-------------------------------------------
+file name   : bioconductor-glmgampoi-1.12.2-r43hf17093f_0.tar.bz2
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+md5         : d59f508307e7995428557c84533adbac
+timestamp   : 2023-07-12 10:50:16 UTC
+dependencies: 
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+-------------------------------------------
+file name   : bioconductor-glmgampoi-1.14.0-r43hf17093f_0.tar.bz2
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-glmgampoi-1.14.0-r43hf17093f_0.tar.bz2
+md5         : f949686982f61bb5eb878c4cca2aa4eb
+timestamp   : 2023-12-15 20:52:49 UTC
+dependencies: 
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+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0a0
+  - libblas >=3.9.0,<4.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-go.db.manual_bundle.txt

@@ -0,0 +1,419 @@
+# Tool: bioconductor-go.db
+software_name: bioconductor-go.db
+tier: T1
+domain: t1_backfill_overall
+downloads: 215677
+summary: A set of annotation maps describing the entire Gene Ontology
+description: A set of annotation maps describing the entire Gene Ontology assembled using data from GO
+dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/data/annotation/html/GO.db.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/data/annotation/html/GO.db.html
+Bioconductor - GO.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages GO.db GO.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see GO.db . A set of annotation maps describing the entire Gene Ontology DOI: 10.18129/B9.bioc.GO.db Bioconductor version: 3.22 A set of annotation maps describing the entire Gene Ontology assembled using data from GO Author: Marc Carlson Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("GO.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GO.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , FunctionalAnnotation Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI Linking To Enhances Depends On Me annaffy , BicARE , geneXtendeR , goProfiles , goTools , SemDist , topGO , Homo.sapiens , Mus.musculus , Rattus.norvegicus , davidTiling , RnaSeqGeneEdgeRQL , OSCA.basic Imports Me ADAM , ADAMgui , adSplit , bioCancer , BioNAR , clusterProfiler , CNEr , compEpiTools , consICA , EnrichmentBrowser , famat , gage , GeneTonic , GenomicInteractionNodes , GOpro , GOSemSim , goseq , goSTAG , GOstats , goTools , ideal , MCbiclust , methylGSA , missMethyl , mosdef , NetSAM , NoRCE , pcaExplorer , Pigengene , rGREAT , rgsepd , rrvgo , simplifyEnrichment , ViSEAGO , ExpHunterSuite Suggests Me annotate , AnnotationDbi , AnnotationForge , appreci8R , BiocSet , Category , categoryCompare , ChIPpeakAnno , dmGsea , esetVis , fgga , FGNet , GlobalAncova , globaltest , goSorensen , GSEABase , hpar , InteractiveComplexHeatmap , interactiveDisplay , iSEEpathways , iSEEu , limma , MetMashR , mgsa , MLP , netZooR , oppar , phenoTest , pRoloc , rols , RTopper , safe , scde , simona , sparrow , SpliceWiz , systemPipeR , TFutils , BioMartGOGeneSets , SomaScan.db , chipenrich.data , msigdb , RforProteomics , yeastExpData , BaseSet , CALANGO , clValid , conos , corrselect , DrDimont , goat , maGUI , pagoda2 , PathwayVote , randomGODB , sand , scITD Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package GO.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/GO.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-go.db --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-go.db 3.2.2 0
+--------------------------
+file name   : bioconductor-go.db-3.2.2-0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.2.2
+build       : 0
+build number: 0
+size        : 25.2 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.2.2-0.tar.bz2
+md5         : 7b3c17ffcebbdedd6cdc33f9d4ad6e8f
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.18
+  - r >=2.7.0
+
+
+bioconductor-go.db 3.3.0 r3.3.1_0
+---------------------------------
+file name   : bioconductor-go.db-3.3.0-r3.3.1_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.3.0
+build       : r3.3.1_0
+build number: 0
+size        : 25.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.3.0-r3.3.1_0.tar.bz2
+md5         : 99e618b71ceac3d8bcb9ea21aa4cbcbd
+dependencies: 
+  - bioconductor-annotationdbi >=1.33.10
+  - r 3.3.1*
+
+
+bioconductor-go.db 3.4.0 r3.3.1_0
+---------------------------------
+file name   : bioconductor-go.db-3.4.0-r3.3.1_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.4.0
+build       : r3.3.1_0
+build number: 0
+size        : 25.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.3.1_0.tar.bz2
+md5         : b9895d06a6b294b9542b93541c6424ae
+dependencies: 
+  - bioconductor-annotationdbi >=1.35.4
+  - r-base 3.3.1*
+
+
+bioconductor-go.db 3.4.0 r3.3.2_0
+---------------------------------
+file name   : bioconductor-go.db-3.4.0-r3.3.2_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.4.0
+build       : r3.3.2_0
+build number: 0
+size        : 25.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.3.2_0.tar.bz2
+md5         : 16f1a1af80bfea4775f2261d4ac4361c
+dependencies: 
+  - bioconductor-annotationdbi >=1.35.4
+  - r-base 3.3.2*
+
+
+bioconductor-go.db 3.4.0 r3.4.1_0
+---------------------------------
+file name   : bioconductor-go.db-3.4.0-r3.4.1_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.4.0
+build       : r3.4.1_0
+build number: 0
+size        : 25.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.0-r3.4.1_0.tar.bz2
+md5         : e56cc4f28b510b537646ae89c0eff3bb
+dependencies: 
+  - bioconductor-annotationdbi >=1.35.4
+  - r-base 3.4.1*
+
+
+bioconductor-go.db 3.4.1 r3.4.1_0
+---------------------------------
+file name   : bioconductor-go.db-3.4.1-r3.4.1_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.4.1
+build       : r3.4.1_0
+build number: 0
+size        : 4 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.4.1-r3.4.1_0.tar.bz2
+md5         : 25a294d2450680c82e6b9ffe634c83c7
+dependencies: 
+  - bioconductor-annotationdbi >=1.37.4
+  - r-base 3.4.1*
+  - wget
+
+
+bioconductor-go.db 3.5.0 r3.4.1_0
+---------------------------------
+file name   : bioconductor-go.db-3.5.0-r3.4.1_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.5.0
+build       : r3.4.1_0
+build number: 0
+size        : 5 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.5.0-r3.4.1_0.tar.bz2
+md5         : b30aed35aa10d7349e273a5b1e189dd0
+dependencies: 
+  - bioconductor-annotationdbi >=1.39.3
+  - r-base 3.4.1*
+  - wget
+
+
+bioconductor-go.db 3.5.0 r3.4.1_1
+---------------------------------
+file name   : bioconductor-go.db-3.5.0-r3.4.1_1.tar.bz2
+name        : bioconductor-go.db
+version     : 3.5.0
+build       : r3.4.1_1
+build number: 1
+size        : 5 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.5.0-r3.4.1_1.tar.bz2
+md5         : 34aaed8458778e3988ad9417cedf06f9
+dependencies: 
+  - bioconductor-annotationdbi >=1.39.3
+  - r-base 3.4.1*
+  - wget
+
+
+bioconductor-go.db 3.6.0 r341_0
+-------------------------------
+file name   : bioconductor-go.db-3.6.0-r341_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.6.0
+build       : r341_0
+build number: 0
+size        : 6 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.6.0-r341_0.tar.bz2
+md5         : c2c0a46d9edbc3405066d095abd11281
+timestamp   : 2018-10-18 13:30:50 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - r-base >=3.4.1,<3.4.2.0a0
+  - wget
+
+
+bioconductor-go.db 3.6.0 r351_0
+-------------------------------
+file name   : bioconductor-go.db-3.6.0-r351_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.6.0
+build       : r351_0
+build number: 0
+size        : 6 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-go.db-3.6.0-r351_0.tar.bz2
+md5         : 59e7a7f27eecb063ee556cb451d4554d
+timestamp   : 2018-10-18 13:32:28 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-go.db 3.7.0 r351_0
+-------------------------------
+file name   : bioconductor-go.db-3.7.0-r351_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.7.0
+build       : r351_0
+build number: 0
+size        : 6 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.7.0-r351_0.tar.bz2
+md5         : 71359a0620f7033708d384a525362d15
+timestamp   : 2018-12-24 12:34:37 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.44.0,<1.45.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-go.db 3.8.2 r36_1
+------------------------------
+file name   : bioconductor-go.db-3.8.2-r36_1.tar.bz2
+name        : bioconductor-go.db
+version     : 3.8.2
+build       : r36_1
+build number: 1
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.8.2-r36_1.tar.bz2
+md5         : 1e2f7577b4aba6cf173dcc8a2f8b0d39
+timestamp   : 2019-08-03 20:56:31 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.46.0,<1.47.0
+  - curl
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-go.db 3.10.0 r36_0
+-------------------------------
+file name   : bioconductor-go.db-3.10.0-r36_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.10.0
+build       : r36_0
+build number: 0
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.10.0-r36_0.tar.bz2
+md5         : 0d305f6b62a862e1c4ce1777647467e3
+timestamp   : 2019-11-03 17:19:18 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.48.0,<1.49.0
+  - curl
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-go.db 3.11.1 r40_0
+-------------------------------
+file name   : bioconductor-go.db-3.11.1-r40_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.11.1
+build       : r40_0
+build number: 0
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.11.1-r40_0.tar.bz2
+md5         : eecf5b3f2fca016622200e7664484264
+timestamp   : 2020-05-11 19:23:17 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.50.0,<1.51.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-go.db 3.11.4 r40_0
+-------------------------------
+file name   : bioconductor-go.db-3.11.4-r40_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.11.4
+build       : r40_0
+build number: 0
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.11.4-r40_0.tar.bz2
+md5         : 7e93e9f3e4f6c22366d9e8961abb975c
+timestamp   : 2020-06-02 19:08:45 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.50.0,<1.51.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-go.db 3.12.1 r40_0
+-------------------------------
+file name   : bioconductor-go.db-3.12.1-r40_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.12.1
+build       : r40_0
+build number: 0
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.12.1-r40_0.tar.bz2
+md5         : 88ffc265fcdedb44a7b26bf7ec5e320a
+timestamp   : 2020-11-01 19:56:18 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-go.db 3.12.1 r40hdfd78af_1
+---------------------------------------
+file name   : bioconductor-go.db-3.12.1-r40hdfd78af_1.tar.bz2
+name        : bioconductor-go.db
+version     : 3.12.1
+build       : r40hdfd78af_1
+build number: 1
+size        : 7 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.12.1-r40hdfd78af_1.tar.bz2
+md5         : 73dfffb253d44f2e239ad0c3a96206c3
+timestamp   : 2021-03-30 15:32:59 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-go.db 3.13.0 r41hdfd78af_0
+---------------------------------------
+file name   : bioconductor-go.db-3.13.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.13.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 8 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.13.0-r41hdfd78af_0.tar.bz2
+md5         : 397957325b84ccaf0402bed0906704af
+timestamp   : 2021-06-03 14:57:27 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.54.0,<1.55.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-go.db 3.14.0 r41hdfd78af_0
+---------------------------------------
+file name   : bioconductor-go.db-3.14.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.14.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 8 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.14.0-r41hdfd78af_0.tar.bz2
+md5         : 09f592f871746d7e8885d85d0ae204f9
+timestamp   : 2021-11-06 07:41:34 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.56.0,<1.57.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-go.db 3.14.0 r41hdfd78af_1
+---------------------------------------
+file name   : bioconductor-go.db-3.14.0-r41hdfd78af_1.tar.bz2
+name        : bioconductor-go.db
+version     : 3.14.0
+build       : r41hdfd78af_1
+build number: 1
+size        : 9 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.14.0-r41hdfd78af_1.tar.bz2
+md5         : 5609fa622e907ab52616aeac57d74ba7
+timestamp   : 2022-08-21 19:50:50 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.56.0,<1.57.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-go.db 3.16.0 r42hdfd78af_0
+---------------------------------------
+file name   : bioconductor-go.db-3.16.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-go.db
+version     : 3.16.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 8 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-go.db-3.16.0-r42hdfd78af_0.tar.bz2
+md5         : 7e8f6bb781a17c51da470164d43372f2
+timestamp   : 2022-11-06 22:41:58 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.60.0,<1.61.0
+  - bioconductor-d

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-hdf5array.manual_bundle.txt

@@ -0,0 +1,372 @@
+# Tool: bioconductor-hdf5array
+software_name: bioconductor-hdf5array
+tier: T1
+domain: t1_backfill_overall
+downloads: 386605
+summary: HDF5 datasets as array-like objects in R
+description: The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-h5mread >=1.2.0,<1.3.0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-rhdf5 >=2.54.0,<2.55.0, bioconductor-s4arrays >=1.10.0,<1.11.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-sparsearray >=1.10.0,<1.11.0, r-base >=4.5,<4.6.0a0, r-matrix
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: http://bioconductor.org/packages/3.6/bioc/html/HDF5Array.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### http://bioconductor.org/packages/3.6/bioc/html/HDF5Array.html
+Bioconductor - HDF5Array About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.6 Software Packages HDF5Array HDF5Array This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see HDF5Array . HDF5 back end for DelayedArray objects DOI: 10.18129/B9.bioc.HDF5Array Bioconductor version: 3.6 An array-like container for convenient access and manipulation of HDF5 datasets. Supports delayed operations and block processing. Author: Hervé Pagès Maintainer: Hervé Pagès &#x3c;&#x68;&#x70;&#x61;&#x67;&#x65;&#x73;&#x20;&#x61;&#x74;&#x20;&#x66;&#x72;&#x65;&#x64;&#x68;&#x75;&#x74;&#x63;&#x68;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("HDF5Array") ): Installation To install this package, start R (version "3.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HDF5Array") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews Annotation , Coverage , DataRepresentation , GenomeAnnotation , Infrastructure , Sequencing , Software Version 1.6.0 In Bioconductor since BioC 3.3 (R-3.3) (8 years) License Artistic-2.0 Depends R (>= 3.4), methods, DelayedArray (>= 0.3.18), rhdf5 Imports utils, tools, BiocGenerics , S4Vectors , IRanges System Requirements URL See More Suggests h5vcData , SummarizedExperiment (>= 1.5.6), GenomicRanges , BiocStyle Linking To Enhances Depends On Me Imports Me beachmat , bsseq Suggests Me DelayedArray , DelayedMatrixStats , MultiAssayExperiment , scran , SummarizedExperiment Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package HDF5Array_1.6.0.tar.gz Windows Binary HDF5Array_1.6.0.zip Mac OS X 10.11 (El Capitan) HDF5Array_1.6.0.tgz Source Repository git clone https://git.bioconductor.org/packages/HDF5Array Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HDF5Array Package Short Url https://bioconductor.org/packages/HDF5Array/ Package Downloads Report Download Stats Old Source Packages for BioC 3.6 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-hdf5array --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-hdf5array 1.6.0 r3.4.1_0
+-------------------------------------
+file name   : bioconductor-hdf5array-1.6.0-r3.4.1_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.6.0
+build       : r3.4.1_0
+build number: 0
+size        : 7.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.6.0-r3.4.1_0.tar.bz2
+md5         : 9ce3089d8bdad38ec1382506b1df0270
+dependencies: 
+  - bioconductor-biocgenerics
+  - bioconductor-delayedarray >=0.3.18
+  - bioconductor-iranges
+  - bioconductor-rhdf5
+  - bioconductor-s4vectors
+  - r-base 3.4.1*
+
+
+bioconductor-hdf5array 1.8.1 r341_0
+-----------------------------------
+file name   : bioconductor-hdf5array-1.8.1-r341_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.8.1
+build       : r341_0
+build number: 0
+size        : 7.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.8.1-r341_0.tar.bz2
+md5         : 5a29f8c1a9be4a76fb99d8b4389f1b63
+timestamp   : 2018-10-12 14:09:02 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - bioconductor-delayedarray >=0.6.6,<0.8.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-rhdf5 >=2.24.0,<2.26.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-hdf5array 1.8.1 r351_0
+-----------------------------------
+file name   : bioconductor-hdf5array-1.8.1-r351_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.8.1
+build       : r351_0
+build number: 0
+size        : 7.9 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.8.1-r351_0.tar.bz2
+md5         : 7b91ab346e6c23be5d4799e588f2403f
+timestamp   : 2018-10-12 14:10:44 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - bioconductor-delayedarray >=0.6.6,<0.8.0
+  - bioconductor-iranges >=2.14.12,<2.16.0
+  - bioconductor-rhdf5 >=2.24.0,<2.26.0
+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-hdf5array 1.10.1 r351_0
+------------------------------------
+file name   : bioconductor-hdf5array-1.10.1-r351_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.10.1
+build       : r351_0
+build number: 0
+size        : 8.1 MB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-hdf5array-1.10.1-r351_0.tar.bz2
+md5         : 3c9076ef86c50cb5ed20c571caac35e9
+timestamp   : 2018-12-11 16:20:59 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.28.0,<0.29.0
+  - bioconductor-delayedarray >=0.8.0,<0.9.0
+  - bioconductor-iranges >=2.16.0,<2.17.0
+  - bioconductor-rhdf5 >=2.26.0,<2.27.0
+  - bioconductor-s4vectors >=0.20.0,<0.21.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-hdf5array 1.12.1 r36h516909a_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.12.1
+build       : r36h516909a_0
+build number: 0
+size        : 9.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.12.1-r36h516909a_0.tar.bz2
+md5         : dc387003cb6b9afc3ab4656574d11993
+timestamp   : 2019-07-24 16:10:30 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.30.0,<0.31.0
+  - bioconductor-delayedarray >=0.10.0,<0.11.0
+  - bioconductor-iranges >=2.18.0,<2.19.0
+  - bioconductor-rhdf5 >=2.28.0,<2.29.0
+  - bioconductor-rhdf5lib >=1.6.0,<1.7.0
+  - bioconductor-s4vectors >=0.22.0,<0.23.0
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-hdf5array 1.14.0 r36h516909a_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.14.0-r36h516909a_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.14.0
+build       : r36h516909a_0
+build number: 0
+size        : 9.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.14.0-r36h516909a_0.tar.bz2
+md5         : 8300d405a29b4f07992b852c07120eb9
+timestamp   : 2019-11-02 13:25:32 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.32.0,<0.33.0
+  - bioconductor-delayedarray >=0.12.0,<0.13.0
+  - bioconductor-iranges >=2.20.0,<2.21.0
+  - bioconductor-rhdf5 >=2.30.0,<2.31.0
+  - bioconductor-rhdf5lib >=1.8.0,<1.9.0
+  - bioconductor-s4vectors >=0.24.0,<0.25.0
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.16.0 r40h037d062_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.16.0-r40h037d062_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.16.0
+build       : r40h037d062_0
+build number: 0
+size        : 9.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.16.0-r40h037d062_0.tar.bz2
+md5         : db7e1d345d97b612e4db407afc446ca7
+timestamp   : 2020-05-10 00:01:37 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.34.0,<0.35.0
+  - bioconductor-delayedarray >=0.14.0,<0.15.0
+  - bioconductor-iranges >=2.22.0,<2.23.0
+  - bioconductor-rhdf5 >=2.32.0,<2.33.0
+  - bioconductor-rhdf5lib >=1.10.0,<1.11.0
+  - bioconductor-s4vectors >=0.26.0,<0.27.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.18.0 r40h037d062_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.18.0-r40h037d062_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.18.0
+build       : r40h037d062_0
+build number: 0
+size        : 9.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.18.0-r40h037d062_0.tar.bz2
+md5         : 6f104a452a31abab224b22234071395a
+timestamp   : 2020-10-29 23:45:19 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.36.0,<0.37.0
+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-iranges >=2.24.0,<2.25.0
+  - bioconductor-rhdf5 >=2.34.0,<2.35.0
+  - bioconductor-rhdf5lib >=1.12.0,<1.13.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.18.1 r40hd029910_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.18.1-r40hd029910_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.18.1
+build       : r40hd029910_0
+build number: 0
+size        : 9.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.18.1-r40hd029910_0.tar.bz2
+md5         : 8394856cad2205d4d4764eec838111a3
+timestamp   : 2021-03-28 21:07:33 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.36.0,<0.37.0
+  - bioconductor-delayedarray >=0.16.0,<0.17.0
+  - bioconductor-iranges >=2.24.0,<2.25.0
+  - bioconductor-rhdf5 >=2.34.0,<2.35.0
+  - bioconductor-rhdf5lib >=1.12.0,<1.13.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.20.0 r41ha2fdcc6_1
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.20.0-r41ha2fdcc6_1.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.20.0
+build       : r41ha2fdcc6_1
+build number: 1
+size        : 9.9 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.20.0-r41ha2fdcc6_1.tar.bz2
+md5         : 75da6543a516cacb2cd3fe94832afde3
+timestamp   : 2021-10-23 22:42:18 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.38.0,<0.39.0
+  - bioconductor-delayedarray >=0.18.0,<0.19.0
+  - bioconductor-iranges >=2.26.0,<2.27.0
+  - bioconductor-rhdf5 >=2.36.0,<2.37.0
+  - bioconductor-rhdf5filters >=1.4.0,<1.5.0
+  - bioconductor-rhdf5lib >=1.14.0,<1.15.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - openssl >=1.1.1l,<1.1.2a
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.20.0 r41hd029910_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.20.0-r41hd029910_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.20.0
+build       : r41hd029910_0
+build number: 0
+size        : 9.9 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.20.0-r41hd029910_0.tar.bz2
+md5         : 314dd7495746ec46c65b6058951d9cbd
+timestamp   : 2021-06-01 06:35:50 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.38.0,<0.39.0
+  - bioconductor-delayedarray >=0.18.0,<0.19.0
+  - bioconductor-iranges >=2.26.0,<2.27.0
+  - bioconductor-rhdf5 >=2.36.0,<2.37.0
+  - bioconductor-rhdf5filters >=1.4.0,<1.5.0
+  - bioconductor-rhdf5lib >=1.14.0,<1.15.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.22.0 r41ha2fdcc6_1
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.22.0-r41ha2fdcc6_1.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.22.0
+build       : r41ha2fdcc6_1
+build number: 1
+size        : 9.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.0-r41ha2fdcc6_1.tar.bz2
+md5         : 8307d33623bacc139b2df14c492e8a70
+timestamp   : 2021-11-07 13:07:40 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.40.0,<0.41.0
+  - bioconductor-delayedarray >=0.20.0,<0.21.0
+  - bioconductor-iranges >=2.28.0,<2.29.0
+  - bioconductor-rhdf5 >=2.38.0,<2.39.0
+  - bioconductor-rhdf5filters >=1.6.0,<1.7.0
+  - bioconductor-rhdf5lib >=1.16.0,<1.17.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - openssl >=1.1.1l,<1.1.2a
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.22.1 r41h5c21468_0
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.22.1-r41h5c21468_0.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.22.1
+build       : r41h5c21468_0
+build number: 0
+size        : 9.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.1-r41h5c21468_0.tar.bz2
+md5         : 40efbcbe24bbd284d8a341b3a999a860
+timestamp   : 2022-02-26 20:29:00 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.40.0,<0.41.0
+  - bioconductor-delayedarray >=0.20.0,<0.21.0
+  - bioconductor-iranges >=2.28.0,<2.29.0
+  - bioconductor-rhdf5 >=2.38.0,<2.39.0
+  - bioconductor-rhdf5filters >=1.6.0,<1.7.0
+  - bioconductor-rhdf5lib >=1.16.0,<1.17.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-hdf5array 1.22.1 r41hc0cfd56_1
+-------------------------------------------
+file name   : bioconductor-hdf5array-1.22.1-r41hc0cfd56_1.tar.bz2
+name        : bioconductor-hdf5array
+version     : 1.22.1
+build       : r41hc0cfd56_1
+build number: 1
+size        : 9.9 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-hdf5array-1.22.1-r41hc0cfd56_1.tar.bz2
+md5         : bc5a371b218f38b78c2ff13de25dd0ff
+time

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcdatasets.manual_bundle.txt

@@ -0,0 +1,225 @@
+# Tool: bioconductor-imcdatasets
+software_name: bioconductor-imcdatasets
+tier: T1
+domain: spatial_transcriptomics
+downloads: 11629
+summary: Collection of publicly available imaging mass cytometry (IMC) datasets
+description: The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.
+dependencies: bioconductor-cytomapper >=1.22.0,<1.23.0, bioconductor-data-packages >=20260207, bioconductor-delayedarray >=0.36.0,<0.37.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.13/data/experiment/html/imcdatasets.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.13/data/experiment/html/imcdatasets.html
+40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images." /> Bioconductor - imcdatasets About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.13 Experiment Packages imcdatasets imcdatasets This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see imcdatasets . Collection of publicly available imaging mass cytometry (IMC) datasets DOI: 10.18129/B9.bioc.imcdatasets Bioconductor version: 3.13 The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images. Author: Nicolas Damond [aut, cre] , Nils Eling [ctb] , Fischer Jana [ctb] Maintainer: Nicolas Damond &#x3c;&#x6e;&#x69;&#x63;&#x6f;&#x6c;&#x61;&#x73;&#x2e;&#x64;&#x61;&#x6d;&#x6f;&#x6e;&#x64;&#x20;&#x61;&#x74;&#x20;&#x64;&#x71;&#x62;&#x6d;&#x2e;&#x75;&#x7a;&#x68;&#x2e;&#x63;&#x68;&#x3e; Citation (from within R, enter citation("imcdatasets") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("imcdatasets") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("imcdatasets") Accessing IMC datasets HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , PackageTypeData , SingleCellData , TechnologyData , Tissue Version 1.0.1 License GPL-3 Depends R (>= 4.1), SingleCellExperiment , cytomapper Imports methods, utils, ExperimentHub , S4Vectors , DelayedArray , HDF5Array System Requirements URL https://github.com/BodenmillerGroup/imcdatasets Bug Reports https://github.com/BodenmillerGroup/imcdatasets/issues See More Suggests BiocStyle , knitr, rmarkdown, markdown, testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package imcdatasets_1.0.1.tar.gz Windows Binary macOS 10.13 (High Sierra) Source Repository git clone https://git.bioconductor.org/packages/imcdatasets Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/imcdatasets Package Short Url https://bioconductor.org/packages/imcdatasets/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-imcdatasets --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-imcdatasets 1.0.0 r41hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-imcdatasets-1.0.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.0.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.0.0-r41hdfd78af_0.tar.bz2
+md5         : adbe4ab042984d9d357bf6a1c7521941
+timestamp   : 2021-06-03 21:28:28 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.4.0,<1.5.0
+  - bioconductor-delayedarray >=0.18.0,<0.19.0
+  - bioconductor-experimenthub >=2.0.0,<2.1.0
+  - bioconductor-hdf5array >=1.20.0,<1.21.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - bioconductor-singlecellexperiment >=1.14.0,<1.15.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-imcdatasets 1.2.0 r41hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-imcdatasets-1.2.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.2.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.2.0-r41hdfd78af_0.tar.bz2
+md5         : 21bd3f37658dfb095b55945512a5712b
+timestamp   : 2021-11-07 20:17:14 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.6.0,<1.7.0
+  - bioconductor-delayedarray >=0.20.0,<0.21.0
+  - bioconductor-experimenthub >=2.2.0,<2.3.0
+  - bioconductor-hdf5array >=1.22.0,<1.23.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-imcdatasets 1.2.0 r41hdfd78af_1
+--------------------------------------------
+file name   : bioconductor-imcdatasets-1.2.0-r41hdfd78af_1.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.2.0
+build       : r41hdfd78af_1
+build number: 1
+size        : 21 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.2.0-r41hdfd78af_1.tar.bz2
+md5         : 8ea956714a1e768cb05ab2cc39a3b1e4
+timestamp   : 2022-09-02 02:27:29 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.6.0,<1.7.0
+  - bioconductor-delayedarray >=0.20.0,<0.21.0
+  - bioconductor-experimenthub >=2.2.0,<2.3.0
+  - bioconductor-hdf5array >=1.22.0,<1.23.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-imcdatasets 1.6.0 r42hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-imcdatasets-1.6.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.6.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 21 KB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.6.0-r42hdfd78af_0.tar.bz2
+md5         : ac6068fc47e38ddc37d5543a956d8326
+timestamp   : 2022-11-09 10:04:50 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.10.0,<1.11.0
+  - bioconductor-data-packages >=20221108
+  - bioconductor-delayedarray >=0.24.0,<0.25.0
+  - bioconductor-experimenthub >=2.6.0,<2.7.0
+  - bioconductor-hdf5array >=1.26.0,<1.27.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - bioconductor-singlecellexperiment >=1.20.0,<1.21.0
+  - bioconductor-spatialexperiment >=1.8.0,<1.9.0
+  - curl
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-imcdatasets 1.8.0 r43hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-imcdatasets-1.8.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.8.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 22 KB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.8.0-r43hdfd78af_0.tar.bz2
+md5         : 09903ee65d7ea5726255d6090997231d
+timestamp   : 2023-07-17 10:41:17 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.12.0,<1.13.0
+  - bioconductor-data-packages >=20230706
+  - bioconductor-delayedarray >=0.26.0,<0.27.0
+  - bioconductor-experimenthub >=2.8.0,<2.9.0
+  - bioconductor-hdf5array >=1.28.0,<1.29.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-imcdatasets 1.10.0 r43hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-imcdatasets-1.10.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.10.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 22 KB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.10.0-r43hdfd78af_0.tar.bz2
+md5         : 6e900b6e139c649f20680093640c393c
+timestamp   : 2023-12-08 12:47:53 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.14.0,<1.15.0
+  - bioconductor-data-packages >=20231203
+  - bioconductor-delayedarray >=0.28.0,<0.29.0
+  - bioconductor-experimenthub >=2.10.0,<2.11.0
+  - bioconductor-hdf5array >=1.30.0,<1.31.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-imcdatasets 1.14.0 r44hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-imcdatasets-1.14.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-imcdatasets
+version     : 1.14.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 21 KB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.14.0-r44hdfd78af_0.tar.bz2
+md5         : ca98d539f9d5da52f48fc64e28a80abb
+timestamp   : 2024-12-22 22:58:04 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.18.0,<1.19.0
+  - bioconductor-data-packages >=20241103
+  - bioconductor-delayedarray >=0.32.0,<0.33.0
+  - bioconductor-experimenthub >=2.14.0,<2.15.0
+  - bioconductor-hdf5array >=1.34.0,<1.35.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-singlecellexperiment >=1.28.0,<1.29.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - curl
+  - r-base >=4.4,<4.5.0a0
+
+
+bioconductor-imcdatasets 1.18.0 r45hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-imcdatasets-1.18.0-r45hdfd78af_0.conda
+name        : bioconductor-imcdatasets
+version     : 1.18.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 24 KB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcdatasets-1.18.0-r45hdfd78af_0.conda
+md5         : 31b8659d420ee000ead4a1a33914055e
+timestamp   : 2026-03-03 01:28:30 UTC
+dependencies: 
+  - bioconductor-cytomapper >=1.22.0,<1.23.0
+  - bioconductor-data-packages >=20260207
+  - bioconductor-delayedarray >=0.36.0,<0.37.0
+  - bioconductor-experimenthub >=3.0.0,<3.1.0
+  - bioconductor-hdf5array >=1.38.0,<1.39.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - curl
+  - r-base >=4.5,<4.6.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-imcrtools.manual_bundle.txt

@@ -0,0 +1,298 @@
+# Tool: bioconductor-imcrtools
+software_name: bioconductor-imcrtools
+tier: T1
+domain: spatial_transcriptomics
+downloads: 8426
+summary: Methods for imaging mass cytometry data analysis
+description: This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
+dependencies: bioconductor-biocneighbors >=2.4.0,<2.5.0, bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-cytomapper >=1.22.0,<1.23.0, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-matrixgenerics >=1.22.0,<1.23.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scuttle >=1.20.0,<1.21.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-abind, r-base >=4.5,<4.6.0a0, r-concaveman, r-data.table, r-distances, r-dplyr, r-dt, r-ggplot2, r-ggraph, r-igraph, r-magrittr, r-pheatmap, r-readr, r-rlang, r-rtriangle, r-sf, r-stringr, r-tidygraph, r-tidyselect, r-viridis, r-vroom
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.14/bioc/html/imcRtools.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.14/bioc/html/imcRtools.html
+Bioconductor - imcRtools About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages imcRtools imcRtools This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see imcRtools . Methods for imaging mass cytometry data analysis DOI: 10.18129/B9.bioc.imcRtools Bioconductor version: 3.14 This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected. Author: Nils Eling [aut, cre] , Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb] Maintainer: Nils Eling &#x3c;&#x6e;&#x69;&#x6c;&#x73;&#x2e;&#x65;&#x6c;&#x69;&#x6e;&#x67;&#x20;&#x61;&#x74;&#x20;&#x64;&#x71;&#x62;&#x6d;&#x2e;&#x75;&#x7a;&#x68;&#x2e;&#x63;&#x68;&#x3e; Citation (from within R, enter citation("imcRtools") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("imcRtools") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("imcRtools") Tools for IMC data analysis HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , DataImport , ImmunoOncology , SingleCell , Software , Spatial Version 1.0.2 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License GPL-3 Depends R (>= 4.1), SpatialExperiment Imports S4Vectors , stats, utils, SummarizedExperiment , methods, pheatmap, scuttle , stringr, readr, EBImage , cytomapper , abind, BiocParallel , viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment , vroom, BiocNeighbors , RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman System Requirements URL https://github.com/BodenmillerGroup/imcRtools Bug Reports https://github.com/BodenmillerGroup/imcRtools/issues See More Suggests CATALYST , grid, tidyr, BiocStyle , knitr, rmarkdown, markdown, testthat Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package imcRtools_1.0.2.tar.gz Windows Binary imcRtools_1.0.2.zip macOS 10.13 (High Sierra) imcRtools_1.0.2.tgz Source Repository git clone https://git.bioconductor.org/packages/imcRtools Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/imcRtools Bioc Package Browser https://code.bioconductor.org/browse/imcRtools/ Package Short Url https://bioconductor.org/packages/imcRtools/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-imcrtools --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-imcrtools 1.0.0 r41hdfd78af_0
+------------------------------------------
+file name   : bioconductor-imcrtools-1.0.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-imcrtools
+version     : 1.0.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 3.6 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.0.0-r41hdfd78af_0.tar.bz2
+md5         : 3ce66873db9ee4be23c8710346d45db4
+timestamp   : 2021-11-08 00:30:35 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.12.0,<1.13.0
+  - bioconductor-biocparallel >=1.28.0,<1.29.0
+  - bioconductor-cytomapper >=1.6.0,<1.7.0
+  - bioconductor-ebimage >=4.36.0,<4.37.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-scuttle >=1.4.0,<1.5.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - bioconductor-spatialexperiment >=1.4.0,<1.5.0
+  - bioconductor-summarizedexperiment >=1.24.0,<1.25.0
+  - r-abind
+  - r-base >=4.1,<4.2.0a0
+  - r-concaveman
+  - r-data.table
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-viridis
+  - r-vroom
+
+
+bioconductor-imcrtools 1.4.0 r42hdfd78af_0
+------------------------------------------
+file name   : bioconductor-imcrtools-1.4.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-imcrtools
+version     : 1.4.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 5.6 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.4.0-r42hdfd78af_0.tar.bz2
+md5         : f8687318d0c4d3f11eeb034495fd4a5b
+timestamp   : 2022-11-06 03:13:41 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.16.0,<1.17.0
+  - bioconductor-biocparallel >=1.32.0,<1.33.0
+  - bioconductor-cytomapper >=1.10.0,<1.11.0
+  - bioconductor-ebimage >=4.40.0,<4.41.0
+  - bioconductor-matrixgenerics >=1.10.0,<1.11.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - bioconductor-scuttle >=1.8.0,<1.9.0
+  - bioconductor-singlecellexperiment >=1.20.0,<1.21.0
+  - bioconductor-spatialexperiment >=1.8.0,<1.9.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - r-abind
+  - r-base >=4.2,<4.3.0a0
+  - r-concaveman
+  - r-data.table
+  - r-distances
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-tidyselect
+  - r-viridis
+  - r-vroom
+
+
+bioconductor-imcrtools 1.6.3 r43hdfd78af_0
+------------------------------------------
+file name   : bioconductor-imcrtools-1.6.3-r43hdfd78af_0.tar.bz2
+name        : bioconductor-imcrtools
+version     : 1.6.3
+build       : r43hdfd78af_0
+build number: 0
+size        : 5.5 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.6.3-r43hdfd78af_0.tar.bz2
+md5         : f77f2bdcf050bb5db3ef5358d5bf822a
+timestamp   : 2023-07-17 11:01:36 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.18.0,<1.19.0
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-cytomapper >=1.12.0,<1.13.0
+  - bioconductor-ebimage >=4.42.0,<4.43.0
+  - bioconductor-matrixgenerics >=1.12.0,<1.13.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-scuttle >=1.10.0,<1.11.0
+  - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - r-abind
+  - r-base >=4.3,<4.4.0a0
+  - r-concaveman
+  - r-data.table
+  - r-distances
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-tidyselect
+  - r-viridis
+  - r-vroom
+
+
+bioconductor-imcrtools 1.8.0 r43hdfd78af_0
+------------------------------------------
+file name   : bioconductor-imcrtools-1.8.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-imcrtools
+version     : 1.8.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 5.6 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.8.0-r43hdfd78af_0.tar.bz2
+md5         : 7104313c1143ceadad2f31ed305e77f9
+timestamp   : 2023-12-12 01:35:50 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=1.20.0,<1.21.0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-cytomapper >=1.14.0,<1.15.0
+  - bioconductor-ebimage >=4.44.0,<4.45.0
+  - bioconductor-matrixgenerics >=1.14.0,<1.15.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-scuttle >=1.12.0,<1.13.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - r-abind
+  - r-base >=4.3,<4.4.0a0
+  - r-concaveman
+  - r-data.table
+  - r-distances
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-tidyselect
+  - r-viridis
+  - r-vroom
+
+
+bioconductor-imcrtools 1.12.0 r44hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-imcrtools-1.12.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-imcrtools
+version     : 1.12.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 5.8 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.12.0-r44hdfd78af_0.tar.bz2
+md5         : b5b9a7aee14359d1072508ce8c1217f5
+timestamp   : 2024-12-22 23:43:07 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=2.0.0,<2.1.0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-cytomapper >=1.18.0,<1.19.0
+  - bioconductor-ebimage >=4.48.0,<4.49.0
+  - bioconductor-matrixgenerics >=1.18.0,<1.19.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-scuttle >=1.16.0,<1.17.0
+  - bioconductor-singlecellexperiment >=1.28.0,<1.29.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - r-abind
+  - r-base >=4.4,<4.5.0a0
+  - r-concaveman
+  - r-data.table
+  - r-distances
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rlang
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-tidyselect
+  - r-viridis
+  - r-vroom
+
+
+bioconductor-imcrtools 1.16.0 r45hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-imcrtools-1.16.0-r45hdfd78af_0.conda
+name        : bioconductor-imcrtools
+version     : 1.16.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 8.4 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-imcrtools-1.16.0-r45hdfd78af_0.conda
+md5         : 4fef003de1b594ddb3de1e3ad34a426e
+timestamp   : 2026-03-02 07:25:34 UTC
+dependencies: 
+  - bioconductor-biocneighbors >=2.4.0,<2.5.0
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-cytomapper >=1.22.0,<1.23.0
+  - bioconductor-ebimage >=4.52.0,<4.53.0
+  - bioconductor-matrixgenerics >=1.22.0,<1.23.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-scuttle >=1.20.0,<1.21.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-abind
+  - r-base >=4.5,<4.6.0a0
+  - r-concaveman
+  - r-data.table
+  - r-distances
+  - r-dplyr
+  - r-dt
+  - r-ggplot2
+  - r-ggraph
+  - r-igraph
+  - r-magrittr
+  - r-pheatmap
+  - r-readr
+  - r-rlang
+  - r-rtriangle
+  - r-sf
+  - r-stringr
+  - r-tidygraph
+  - r-tidyselect
+  - r-viridis
+  - r-vroom

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-interactivedisplaybase.manual_bundle.txt

@@ -0,0 +1,360 @@
+# Tool: bioconductor-interactivedisplaybase
+software_name: bioconductor-interactivedisplaybase
+tier: T1
+domain: t1_backfill_overall
+downloads: 114195
+summary: Base package for enabling powerful shiny web displays of Bioconductor objects
+description: The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, r-base >=4.5,<4.6.0a0, r-dt, r-shiny
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/interactiveDisplayBase.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/interactiveDisplayBase.html
+Bioconductor - interactiveDisplayBase Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages interactiveDisplayBase interactiveDisplayBase This package is deprecated . It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.22 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see interactiveDisplayBase . Base package for enabling powerful shiny web displays of Bioconductor objects DOI: 10.18129/B9.bioc.interactiveDisplayBase Bioconductor version: 3.22 The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects. Author: Bioconductor Package Maintainer [cre], Shawn Balcome [aut], Marc Carlson [ctb], Marcel Ramos [ctb] Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("interactiveDisplayBase") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("interactiveDisplayBase") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("interactiveDisplayBase") Using interactiveDisplayBase for Bioconductor object visualization and modification HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Classification , DataRepresentation , GO , GUI , GeneExpression , Genetics , Microarray , Network , QualityControl , Sequencing , ShinyApps , Software , Visualization Version 1.48.0 In Bioconductor since BioC 3.0 (R-3.1) (11.5 years) License Artistic-2.0 Depends R (>= 2.10), methods, BiocGenerics Imports shiny , DT System Requirements URL See More Suggests knitr , markdown Linking To Enhances rstudioapi Depends On Me Imports Me interactiveDisplay Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package interactiveDisplayBase_1.48.0.tar.gz Windows Binary (x86_64) interactiveDisplayBase_1.48.0.zip macOS Binary (x86_64) interactiveDisplayBase_1.48.0.tgz macOS Binary (arm64) interactiveDisplayBase_1.48.0.tgz Source Repository git clone https://git.bioconductor.org/packages/interactiveDisplayBase Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/interactiveDisplayBase Package Short Url https://bioconductor.org/packages/interactiveDisplayBase/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-interactivedisplaybase --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-interactivedisplaybase 1.12.0 r3.3.1_0
+---------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.12.0-r3.3.1_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.12.0
+build       : r3.3.1_0
+build number: 0
+size        : 25 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.3.1_0.tar.bz2
+md5         : 1fc2ced5356c32f8c80c98bd43a71520
+dependencies: 
+  - bioconductor-biocgenerics
+  - r 3.3.1*
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.12.0 r3.3.2_0
+---------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.12.0-r3.3.2_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.12.0
+build       : r3.3.2_0
+build number: 0
+size        : 27 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.3.2_0.tar.bz2
+md5         : b80c7dac832804a662d378bfac55857f
+dependencies: 
+  - bioconductor-biocgenerics
+  - r-base 3.3.2*
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.12.0 r3.4.1_0
+---------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.12.0-r3.4.1_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.12.0
+build       : r3.4.1_0
+build number: 0
+size        : 29 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.12.0-r3.4.1_0.tar.bz2
+md5         : 7115dae2471123a3f9f372e7548c8286
+dependencies: 
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.14.0 r3.4.1_0
+---------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.14.0-r3.4.1_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.14.0
+build       : r3.4.1_0
+build number: 0
+size        : 38 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.14.0-r3.4.1_0.tar.bz2
+md5         : c41aba3cbcc5cf368a9153bca4e5ec90
+dependencies: 
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.16.0 r3.4.1_0
+---------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.16.0-r3.4.1_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.16.0
+build       : r3.4.1_0
+build number: 0
+size        : 38 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.16.0-r3.4.1_0.tar.bz2
+md5         : 131f82996370f023e9292c219f6872c2
+dependencies: 
+  - bioconductor-biocgenerics
+  - r-base 3.4.1*
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.18.0 r341_0
+-------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.18.0-r341_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.18.0
+build       : r341_0
+build number: 0
+size        : 39 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.18.0-r341_0.tar.bz2
+md5         : 15ef54c687a9db41c3ed5d7b0f75eea4
+timestamp   : 2018-10-12 09:26:24 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - r-base >=3.4.1,<3.4.2.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.18.0 r351_0
+-------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.18.0-r351_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.18.0
+build       : r351_0
+build number: 0
+size        : 45 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-interactivedisplaybase-1.18.0-r351_0.tar.bz2
+md5         : 9ef36f14fbdb6b52445db40408e1428a
+timestamp   : 2018-10-12 09:25:03 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.26.0,<0.28.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.20.0 r351_0
+-------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.20.0-r351_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.20.0
+build       : r351_0
+build number: 0
+size        : 46 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.20.0-r351_0.tar.bz2
+md5         : a14cb9600292881e33267bffab502f43
+timestamp   : 2018-12-10 22:50:28 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.28.0,<0.29.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.22.0 r36_1
+------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.22.0-r36_1.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.22.0
+build       : r36_1
+build number: 1
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.22.0-r36_1.tar.bz2
+md5         : 6de095a07dc7ee041b7b23654a6b6abf
+timestamp   : 2019-07-22 10:11:40 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.30.0,<0.31.0
+  - r-base >=3.6,<3.7.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.24.0 r36_0
+------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.24.0-r36_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.24.0
+build       : r36_0
+build number: 0
+size        : 48 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.24.0-r36_0.tar.bz2
+md5         : a56f2a3fb1ca6572362d96fe4002d230
+timestamp   : 2019-11-01 13:31:43 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.32.0,<0.33.0
+  - r-base >=3.6,<3.7.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.26.0 r40_0
+------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.26.0-r40_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.26.0
+build       : r40_0
+build number: 0
+size        : 48 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.26.0-r40_0.tar.bz2
+md5         : 1469ab7e6fff6cc84ed4266a1fab0bba
+timestamp   : 2020-05-10 06:13:01 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.34.0,<0.35.0
+  - r-base >=4.0,<4.1.0a0
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.28.0 r40_0
+------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.28.0-r40_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
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+build       : r40_0
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+license     : Artistic-2.0
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+  - r-dt
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.28.0 r40hdfd78af_1
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.28.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-interactivedisplaybase
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+md5         : 8d22711f2a43bdbb8dd9c03e9f8f3638
+timestamp   : 2021-03-27 03:04:59 UTC
+dependencies: 
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+  - r-base >=4.0,<4.1.0a0
+  - r-dt
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.30.0 r41hdfd78af_0
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.30.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
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+build       : r41hdfd78af_0
+build number: 0
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.30.0-r41hdfd78af_0.tar.bz2
+md5         : ce7aacead080f18c0fedf03e2176dd81
+timestamp   : 2021-05-31 00:58:27 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.38.0,<0.39.0
+  - r-base >=4.1,<4.2.0a0
+  - r-dt
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.32.0 r41hdfd78af_0
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.32.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.32.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 42 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.32.0-r41hdfd78af_0.tar.bz2
+md5         : d3313430918e1f28648d4052621e65bc
+timestamp   : 2021-11-01 18:07:47 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.40.0,<0.41.0
+  - r-base >=4.1,<4.2.0a0
+  - r-dt
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.36.0 r42hdfd78af_0
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.36.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
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+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.36.0-r42hdfd78af_0.tar.bz2
+md5         : 288ee61d446a563b569b27e1ed6dd308
+timestamp   : 2022-11-03 20:43:50 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.44.0,<0.45.0
+  - r-base >=4.2,<4.3.0a0
+  - r-dt
+  - r-shiny
+
+
+bioconductor-interactivedisplaybase 1.38.0 r43hdfd78af_0
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.38.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.38.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 39 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.38.0-r43hdfd78af_0.tar.bz2
+md5         : ff2f32c8117f1e5ecdfe7ef8d4d4bc86
+timestamp   : 2023-07-07 17:38:16 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.46.0,<0.47.0
+  - r-base >=4.3,<4.4.0a0
+  - r-dt
+  - r-shiny
+
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+bioconductor-interactivedisplaybase 1.40.0 r43hdfd78af_0
+--------------------------------------------------------
+file name   : bioconductor-interactivedisplaybase-1.40.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-interactivedisplaybase
+version     : 1.40.0
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+build number: 0
+size        : 40 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-interactivedisplaybase-1.40.0-r43hdfd78af_0.ta

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-iranges.manual_bundle.txt

@@ -0,0 +1,425 @@
+# Tool: bioconductor-iranges
+software_name: bioconductor-iranges
+tier: T1
+domain: t1_backfill_overall
+downloads: 1839431
+summary: Foundation of integer range manipulation in Bioconductor
+description: Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/IRanges.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=0]
+
+Usage: /path/to/Rscript [--options] [-e expr [-e expr2 ...] | file] [args]
+
+--options accepted are
+  --help              Print usage and exit
+  --version           Print version and exit
+  --verbose           Print information on progress
+  --default-packages=list
+                      Where 'list' is a comma-separated set
+                        of package names, or 'NULL'
+or options to R, in addition to --no-echo --no-restore, such as
+  --save              Do save workspace at the end of the session
+  --no-environ        Don't read the site and user environment files
+  --no-site-file      Don't read the site-wide Rprofile
+  --no-init-file      Don't read the user R profile
+  --restore           Do restore previously saved objects at startup
+  --vanilla           Combine --no-save, --no-restore, --no-site-file
+                        --no-init-file and --no-environ
+
+'file' may contain spaces but not shell metacharacters
+Expressions (one or more '-e <expr>') may be used *instead* of 'file'
+See also  ?Rscript  from within R
+
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/IRanges.html
+Bioconductor - IRanges Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages IRanges IRanges This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see IRanges . Foundation of integer range manipulation in Bioconductor DOI: 10.18129/B9.bioc.IRanges Bioconductor version: 3.22 Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames. Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Michael Lawrence [aut] Maintainer: Hervé Pagès &#x3c;&#x68;&#x70;&#x61;&#x67;&#x65;&#x73;&#x2e;&#x6f;&#x6e;&#x2e;&#x67;&#x69;&#x74;&#x68;&#x75;&#x62;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("IRanges") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("IRanges") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("IRanges") An Overview of the IRanges package PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 2.44.0 In Bioconductor since BioC 2.3 (R-2.8) (17.5 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6) Imports stats4 System Requirements URL https://bioconductor.org/packages/IRanges Bug Reports https://github.com/Bioconductor/IRanges/issues See More Suggests XVector , GenomicRanges , Rsamtools , GenomicAlignments , GenomicFeatures , BSgenome.Celegans.UCSC.ce2 , pasillaBamSubset , RUnit , BiocStyle Linking To S4Vectors Enhances Depends On Me AnnotationDbi , AnnotationHubData , BaalChIP , bambu , biomvRCNS , Biostrings , BiSeq , BSgenome , BSgenomeForge , bumphunter , CAFE , casper , CexoR , chimeraviz , ChIPpeakAnno , chipseq , cigarillo , CODEX , consensusSeekeR , CSAR , CSSQ , customProDB , deepSNV , DelayedArray , DESeq2 , DEXSeq , DirichletMultinomial , DMCFB , DMCHMM , DMRcaller , epigenomix , ExCluster , fCCAC , GenomeInfoDb , GenomicAlignments , GenomicDistributions , GenomicFeatures , GenomicRanges , groHMM , gtrellis , Gviz , HelloRanges , HERON , HiTC , IdeoViz , InTAD , MotifDb , MultimodalExperiment , NADfinder , oncoscanR , ORFik , OTUbase , pepStat , periodicDNA , plyranges , proBAMr , pwalign , RepViz , rGREAT , RJMCMCNucleosomes , RNAmodR , S4Arrays , Scale4C , SCOPE , SGSeq , SICtools , Structstrings , TEQC , traseR , triplex , VariantTools , VplotR , XVector , pd.ag , pd.aragene.1.0.st , pd.aragene.1.1.st , pd.ath1.121501 , pd.barley1 , pd.bovgene.1.0.st , pd.bovgene.1.1.st , pd.bovine , pd.bsubtilis , pd.cangene.1.0.st , pd.cangene.1.1.st , pd.canine , pd.canine.2 , pd.celegans , pd.chicken , pd.chigene.1.0.st , pd.chigene.1.1.st , pd.chogene.2.0.st , pd.chogene.2.1.st , pd.citrus , pd.clariom.d.human , pd.clariom.s.human , pd.clariom.s.human.ht , pd.clariom.s.mouse , pd.clariom.s.mouse.ht , pd.clariom.s.rat , pd.clariom.s.rat.ht , pd.cotton , pd.cyngene.1.0.st , pd.cyngene.1.1.st , pd.cyrgene.1.0.st , pd.cyrgene.1.1.st , pd.cytogenetics.array , pd.drogene.1.0.st , pd.drogene.1.1.st , pd.drosgenome1 , pd.drosophila.2 , pd.e.coli.2 , pd.ecoli , pd.ecoli.asv2 , pd.elegene.1.0.st , pd.elegene.1.1.st , pd.equgene.1.0.st , pd.equgene.1.1.st , pd.felgene.1.0.st , pd.felgene.1.1.st , pd.fingene.1.0.st , pd.fingene.1.1.st , pd.genomewidesnp.5 , pd.genomewidesnp.6 , pd.guigene.1.0.st , pd.guigene.1.1.st , pd.hc.g110 , pd.hg.focus , pd.hg.u133.plus.2 , pd.hg.u133a , pd.hg.u133a.2 , pd.hg.u133a.tag , pd.hg.u133b , pd.hg.u219 , pd.hg.u95a , pd.hg.u95av2 , pd.hg.u95b , pd.hg.u95c , pd.hg.u95d , pd.hg.u95e , pd.hg18.60mer.expr , pd.ht.hg.u133.plus.pm , pd.ht.hg.u133a , pd.ht.mg.430a , pd.hta.2.0 , pd.hu6800 , pd.huex.1.0.st.v2 , pd.hugene.1.0.st.v1 , pd.hugene.1.1.st.v1 , pd.hugene.2.0.st , pd.hugene.2.1.st , pd.maize , pd.mapping250k.nsp , pd.mapping250k.sty , pd.mapping50k.hind240 , pd.mapping50k.xba240 , pd.margene.1.0.st , pd.margene.1.1.st , pd.medgene.1.0.st , pd.medgene.1.1.st , pd.medicago , pd.mg.u74a , pd.mg.u74av2 , pd.mg.u74b , pd.mg.u74bv2 , pd.mg.u74c , pd.mg.u74cv2 , pd.mirna.1.0 , pd.mirna.2.0 , pd.mirna.3.0 , pd.mirna.4.0 , pd.moe430a , pd.moe430b , pd.moex.1.0.st.v1 , pd.mogene.1.0.st.v1 , pd.mogene.1.1.st.v1 , pd.mogene.2.0.st , pd.mogene.2.1.st , pd.mouse430.2 , pd.mouse430a.2 , pd.mta.1.0 , pd.mu11ksuba , pd.mu11ksubb , pd.nugo.hs1a520180 , pd.nugo.mm1a520177 , pd.ovigene.1.0.st , pd.ovigene.1.1.st , pd.pae.g1a , pd.plasmodium.anopheles , pd.poplar , pd.porcine , pd.porgene.1.0.st , pd.porgene.1.1.st , pd.rabgene.1.0.st , pd.rabgene.1.1.st , pd.rae230a , pd.rae230b , pd.raex.1.0.st.v1 , pd.ragene.1.0.st.v1 , pd.ragene.1.1.st.v1 , pd.ragene.2.0.st , pd.ragene.2.1.st , pd.rat230.2 , pd.rcngene.1.0.st , pd.rcngene.1.1.st , pd.rg.u34a , pd.rg.u34b , pd.rg.u34c , pd.rhegene.1.0.st , pd.rhegene.1.1.st , pd.rhesus , pd.rice , pd.rjpgene.1.0.st , pd.rjpgene.1.1.st , pd.rn.u34 , pd.rta.1.0 , pd.rusgene.1.0.st , pd.rusgene.1.1.st , pd.s.aureus , pd.soybean , pd.soygene.1.0.st , pd.soygene.1.1.st , pd.sugar.cane , pd.tomato , pd.u133.x3p , pd.vitis.vinifera , pd.wheat , pd.x.laevis.2 , pd.x.tropicalis , pd.xenopus.laevis , pd.yeast.2 , pd.yg.s98 , pd.zebgene.1.0.st , pd.zebgene.1.1.st , pd.zebrafish , harbChIP , LiebermanAidenHiC2009 Imports Me alabaster.bumpy , alabaster.ranges , alabaster.se , ALDEx2 , AllelicImbalance , amplican , annmap , annotatr , appreci8R , ASpli , AssessORF , ATACseqQC , ATACseqTFEA , atena , ballgown , bamsignals , BBCAnalyzer , beadarray , BgeeCall , BindingSiteFinder , Bioc.gff , biovizBase , biscuiteer , BiSeq , bnbc , branchpointer , breakpointR , bsseq , BUMHMM , BumpyMatrix , BUSpaRse , CAGEfightR , cageminer , CAGEr , cBioPortalData , cfdnakit , cfDNAPro , ChIPanalyser , chipenrich , ChIPexoQual , ChIPseeker , chipseq , ChIPseqR , ChIPsim , ChromHeatMap , ChromSCape , chromVAR , cicero , circRNAprofiler , CircSeqAlignTk , cleanUpdTSeq , cleaver , cn.mops , CNEr , CNVfilteR , CNVMetrics , CNVPanelizer , CNVRanger , CNVrd2 , COCOA , coMethDMR , compEpiTools , ComplexHeatmap , CompoundDb , conumee , CopyNumberPlots , CoverageView , crisprBase , crisprBowtie , crisprDesign , crisprScore , CRISPRseek , CrispRVariants , crisprViz , crupR , csaw , CTexploreR , dada2 , DAMEfinder , debrowser , DECIPHER , deconvR , DegCre , DegNorm , DelayedMatrixStats , deltaCaptureC , demuxSNP , derfinder , derfinderHelper , derfinderPlot , DEScan2 , DiffBind , diffHic , diffUTR , DMRcaller , DMRcate , DMRScan , dmrseq , DNAfusion , DominoEffect , dreamlet , DRIMSeq , DropletUtils , dStruct , easyRNASeq , EDASeq , eisaR , ELMER , ELViS , enhancerHomologSearch , EnrichedHeatmap , ensembldb , EpiCompare , epidecodeR , epigraHMM , EpiMix , epimutacions , epiregulon , epistack , EpiTxDb , epivizr , epivizrData , esATAC , EventPointer , extraChIPs , factR , FastqCleaner , fastseg , fcScan , FilterFFPE , FindIT2 , fishpond , FLAMES , FRASER , G4SNVHunter , GA4GHclient , gcapc , gDNAx , geneAttribution , GENESIS , genomation , GenomAutomorphism , genomeIntervals , GenomicAlignments , GenomicDataCommons , GenomicFiles , GenomicInteractionNodes , GenomicInteractions , GenomicOZone , GenomicPlot , GenomicScores , GenomicTuples , GenVisR , geomeTriD , ggbio , gmapR , gmoviz , GOfuncR , GOpro , GOTHiC , GSVA , GUIDEseq , gVenn , gwascat , h5mread , h5vc , HDF5Array , heatmaps , hermes , HicAggR , HiCaptuRe , HiCBricks , HiCcompare , HiCExperiment , HiContacts , hicVennDiagram , HilbertCurve , hummingbird , icetea , ideal , idr2d , igblastr , InPAS , INSPEcT , intansv , InteractionSet , InteractiveComplexHeatmap , IntEREst , ipdDb , iSEEu , IsoformSwitchAnalyzeR , isomiRs , IVAS , karyoploteR , katdetectr , knowYourCG , linkSet , LOLA , m6Aboost , magpie , mariner , maser , MatrixRider , mCSEA , MDTS , MEAL , MEDIPS , MesKit , metagene2 , metaseqR2 , methimpute , methInheritSim , methodical , MethReg , methrix , methylCC , methylInheritance , methylKit , methylPipe , MethylSeekR , methylSig , methylumi , mia , minfi , MinimumDistance , MIRA , missMethyl , mobileRNA , Modstrings , monaLisa , mosaics , MOSim , Motif2Site , motifbreakR , motifmatchr , MotifPeeker , motifTestR , MouseFM , msa , MSA2dist , MsBackendMassbank , MsBackendMgf , MsBackendMsp , MsBackendRawFileReader , MsBackendSql , MsExperiment , msgbsR , MSnbase , MultiAssayExperiment , MultiDataSet , mumosa , MungeSumstats , musicatk , MutationalPatterns , mutscan , NanoMethViz , NanoStringNCTools , ncRNAtools , normr , nucleoSim , nucleR , nullranges , OGRE , oligoClasses , OmaDB , OMICsPCA , openPrimeR , Organism.dplyr , OrganismDbi , OUTRIDER , OutSplice , packFinder , panelcn.mops , pcaExplorer , pdInfoBuilder , peakCombiner , PhIPData , PICB , plotgardener , plyinteractions , podkat , pqsfinder , pram , prebs , preciseTAD , primirTSS , proActiv , ProteoDisco , PSMatch , PureCN , Pviz , QDNAseq , QFeatures , qpgraph , qPLEXanalyzer , qsea , QuasR , R3CPET , r3Cseq , raer , RaggedExperiment , RAIDS , ramr , RareVariantVis , RCAS , recount , recoup , REDseq , regioneR , regutools , REMP , ReportingTools , RESOLVE , rfaRm , rfPred , RgnTX , RiboCrypt , RiboDiPA , RiboProfiling , riboSeqR , ribosomeProfilingQC , rigvf , rnaEditr , RNAmodR.AlkAnilineSeq , RNAmodR.ML , RNAmodR.RiboMethSeq , RnBeads , roar , rprimer , Rqc , Rsamtools , RSVSim , RTN , rtracklayer , sarks , saseR , SCAN.UPC , scanMiR , scanMiRApp , scDblFinder , scHOT , scPipe , scRNAseqApp , segmenter , segmentSeq , SeqArray , seqCAT , Seqinfo , seqPattern , seqsetvis , SeqSQC , SeqVarTools , sesame , sevenC , ShortRead , signeR , signifinder , SimFFPE , SingleMoleculeFootprinting , sitadela , Site2Target , SMITE , snapcount , SNPhood , SomaticSignatures , SOMNiBUS , SparseArray , SparseSignatures , Spectra , SpectriPy , spiky , SpliceWiz , SplicingGraphs , SPLINTER , srnadiff , STADyUM , strandCheckR , StructuralVariantAnnotation , SummarizedExperiment , SynExtend , tadar , TAPseq , target , TCGAbiolinks , TCGAutils , TCseq , TENET , TFBSTools , TFEA.ChIP , TFHAZ , tidyCoverage , TnT , tracktables , trackViewer , transcriptR , transmogR , TreeSummarizedExperiment , TRESS , tricycle , tRNA , tRNAdbImport , tRNAscanImport , TVTB , txcutr , txdbmaker , tximeta , UMI4Cats , Uniquorn , universalmotif , UPDhmm , VanillaICE , VarCon , VariantAnnotation , VariantExperiment , VariantFiltering , VaSP , VDJdive , vmrseq , wavClusteR , wiggleplotr , xcms , xcore , XVector , yamss , ZygosityPredictor , fitCons.UCSC.hg19 , GenomicState , MafDb.1Kgenomes.phase1.GRCh38 , MafDb.1Kgenomes.phase1.hs37d5 , MafDb.1Kgenomes.phase3.GRCh38 , MafDb.1Kgenomes.phase3.hs37d5 , MafDb.ExAC.r1.0.GRCh38 , MafDb.ExAC.r1.0.hs37d5 , MafDb.ExAC.r1.0.nonTCGA.GRCh38 , MafDb.ExAC.r1.0.nonTCGA.hs37d5 , MafDb.gnomAD.r2.1.GRCh38 , MafDb.gnomAD.r2.1.hs37d5 , MafDb.gnomADex.r2.1.GRCh38 , MafDb.gnomADex.r2.1.hs37d5 , MafDb.TOPMed.freeze5.hg19 , MafDb.TOPMed.freeze5.hg38 , MafH5.gnomAD.v4.0.GRCh38 , pd.081229.hg18.promoter.medip.hx1 , pd.2006.07.18.hg18.refseq.promoter , pd.2006.07.18.mm8.refseq.promoter , pd.2006.10.31.rn34.refseq.promoter , pd.charm.hg18.example , pd.feinberg.hg18.me.hx1 , pd.feinberg.mm8.me.hx1 , pd.mirna.3.1 , phastCons100way.UCSC.hg19 , phastCons100way.UCSC.hg38 , phastCons7way.UCSC.hg38 , SNPlocs.Hsapiens.dbSNP144.GRCh37 , SNPlocs.Hsapiens.dbSNP144.GRCh38 , SNPlocs.Hsapiens.dbSNP149.GRCh38 , SNPlocs.Hsapiens.dbSNP150.GRCh38 , SNPlocs.Hsapiens.dbSNP155.GRCh37 , SNPlocs.Hsapiens.dbSNP155.GRCh38 , XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 , XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 , chipenrich.data , fourDNData , leeBamViews , MethylSeqData , pd.atdschip.tiling , sesameData , SomaticCancerAlterations , spatialLIBD , seqpac , ActiveDriverWGS , alakazam , cpp11bigwig , crispRdesignR , cubar , DESNP , GencoDymo2 , geno2proteo , GenoPop , hahmmr , hoardeR, iimi , karyotapR , lisat , locuszoomr , longreadvqs , LoopRig , MitoHEAR , noisyr , numbat , PACVr , RapidoPGS , refseqR , revert , rnaCrosslinkOO , Signac , TmCalculator , VALERIE Suggests Me annotate , AnnotationHub , BaseSpaceR , BiocGenerics , BREW3R.r , CCAFE , Chicago , ClassifyR , DFplyr , easylift , epivizrChart , gDRcore , gDRutils , Glimma , GWASTools , HilbertVis , HilbertVisGUI , iscream , maftools , martini , MiRaGE , multicrispr , partCNV , plyxp , regionalpcs , regionReport , RTCGA , S4Vectors , SigsPack , splatter , svaNUMT , svaRetro , systemPipeR , TFutils , tidybulk , MetaScope , scMultiome , systemPipeRdata , xcoredata , yeastRNASeq , fuzzyjoin , gggenomes , gkmSVM , MiscMetabar , MoBPS , polyRAD , pQTLdata , rliger , scPloidy , seqmagick , Seurat , sigminer , updog , valr Links To Me Bioc.gff , Biostrings , cigarillo , CNEr , DECIPHER , GenomicAlignments , GenomicRanges , kebabs , MatrixRider , pwalign , Rsamtools , rtracklayer , ShortRead , SparseArray , Structstrings , triplex , VariantAnnotation , VariantFiltering , XVector Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package IRanges_2.44.0.tar.gz Windows Binary (x86_64) IRanges_2.44.0.zip macOS Binary (x86_64) IRanges_2.44.0.tgz macOS Binary (arm64) IRanges_2.44.0.tgz Source Repository git clone https://git.bioconductor.org/packages/IRanges Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IRanges Bioc Package Browser https://code.bioconductor.org/browse/IRanges/ Package Short Url https://bioconductor.org/packages/IRanges/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-iranges --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-iranges 2.2.9 0
+----------------------------
+file name   : bioconductor-iranges-2.2.9-0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.2.9
+build       : 0
+build number: 0
+size        : 1.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.2.9-0.tar.bz2
+md5         : ac08b68017ca9b0ba4522a8e7a4bd42a
+dependencies: 
+  - bioconductor-biocgenerics
+  - bioconductor-s4vectors
+  - r >=3.1.0
+
+
+bioconductor-iranges 2.4.0 0
+----------------------------
+file name   : bioconductor-iranges-2.4.0-0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.4.0
+build       : 0
+build number: 0
+size        : 1.6 MB
+license     : Artistic-2.0
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+md5         : d3420ed6d62570625b87f892f69ee9fd
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+  - r >=3.1.0
+
+
+bioconductor-iranges 2.4.1 0
+----------------------------
+file name   : bioconductor-iranges-2.4.1-0.tar.bz2
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+md5         : 89a8206d5c0f53ff0c2c00e5d2afe1bb
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+  - r >=3.1.0
+
+
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+----------------------------
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+name        : bioconductor-iranges
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+md5         : 819ab4cc7c6f1b8b08bf4f4526a73008
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+----------------------------
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+md5         : fb4e709080781d58b5ac2e657c592f7b
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+
+bioconductor-iranges 2.4.8 0
+----------------------------
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+name        : bioconductor-iranges
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+md5         : 7ee66e351a8b2f3e3b7822a3b3d45341
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+
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+-----------------------------------
+file name   : bioconductor-iranges-2.6.0-r3.3.1_0.tar.bz2
+name        : bioconductor-iranges
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+md5         : f11223044697df893ee955df0b353590
+dependencies: 
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+  - bioconductor-s4vectors >=0.8.4
+  - r 3.3.1*
+
+
+bioconductor-iranges 2.6.1 r3.3.1_0
+-----------------------------------
+file name   : bioconductor-iranges-2.6.1-r3.3.1_0.tar.bz2
+name        : bioconductor-iranges
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+build       : r3.3.1_0
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.6.1-r3.3.1_0.tar.bz2
+md5         : 99b263aa381aacadf1cdb4ad9949f734
+dependencies: 
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+  - r 3.3.1*
+
+
+bioconductor-iranges 2.8.0 r3.3.1_0
+-----------------------------------
+file name   : bioconductor-iranges-2.8.0-r3.3.1_0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.8.0
+build       : r3.3.1_0
+build number: 0
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.0-r3.3.1_0.tar.bz2
+md5         : c29f73ed575e9327d33aff36ce71c3db
+dependencies: 
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+  - bioconductor-s4vectors 0.12.0
+  - r 3.3.1*
+
+
+bioconductor-iranges 2.8.2 r3.3.1_0
+-----------------------------------
+file name   : bioconductor-iranges-2.8.2-r3.3.1_0.tar.bz2
+name        : bioconductor-iranges
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+build       : r3.3.1_0
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.3.1_0.tar.bz2
+md5         : d1dfa8fd7c6a961cfea966c8f7e9e7f2
+dependencies: 
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+  - r-base 3.3.1*
+
+
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+-----------------------------------
+file name   : bioconductor-iranges-2.8.2-r3.3.2_0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.8.2
+build       : r3.3.2_0
+build number: 0
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.3.2_0.tar.bz2
+md5         : a6000e13548b3ec81e1c9b7a22a2d963
+dependencies: 
+  - bioconductor-biocgenerics >=0.19.1
+  - bioconductor-s4vectors >=0.11.19
+  - r-base 3.3.2*
+
+
+bioconductor-iranges 2.8.2 r3.4.1_0
+-----------------------------------
+file name   : bioconductor-iranges-2.8.2-r3.4.1_0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.8.2
+build       : r3.4.1_0
+build number: 0
+size        : 1.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.8.2-r3.4.1_0.tar.bz2
+md5         : 47c82e857deb9f3814a7fc756bda3241
+dependencies: 
+  - bioconductor-biocgenerics >=0.19.1
+  - bioconductor-s4vectors >=0.11.19
+  - r-base 3.4.1*
+
+
+bioconductor-iranges 2.10.5 r3.4.1_0
+------------------------------------
+file name   : bioconductor-iranges-2.10.5-r3.4.1_0.tar.bz2
+name        : bioconductor-iranges
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+build       : r3.4.1_0
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+size        : 1.6 MB
+license     : Artistic-2.0
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+md5         : 755fbc8be4f4ffe6afee1bb28e28869a
+dependencies: 
+  - bioconductor-biocgenerics >=0.21.1
+  - bioconductor-s4vectors >=0.13.17
+  - r-base 3.4.1*
+
+
+bioconductor-iranges 2.12.0 r3.4.1_0
+------------------------------------
+file name   : bioconductor-iranges-2.12.0-r3.4.1_0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.12.0
+build       : r3.4.1_0
+build number: 0
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+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.12.0-r3.4.1_0.tar.bz2
+md5         : d6eba62c90f14eefee3db162c1e9fb26
+dependencies: 
+  - bioconductor-biocgenerics >=0.23.3
+  - bioconductor-s4vectors >=0.15.5
+  - r-base 3.4.1*
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+
+bioconductor-iranges 2.14.12 r341h470a237_0
+-------------------------------------------
+file name   : bioconductor-iranges-2.14.12-r341h470a237_0.tar.bz2
+name        : bioconductor-iranges
+version     : 2.14.12
+build       : r341h470a237_0
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+size        : 1.6 MB
+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.14.12-r341h470a237_0.tar.bz2
+md5         : 62f7abd67d8b218ef1f167a21b3457a7
+timestamp   : 2018-10-12 13:03:33 UTC
+dependencies: 
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+  - bioconductor-s4vectors >=0.18.3,<0.20.0
+  - libgcc-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
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+
+bioconductor-iranges 2.14.12 r351h470a237_0
+-------------------------------------------
+file name   : bioconductor-iranges-2.14.12-r351h470a237_0.tar.bz2
+name        : bioconductor-iranges
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-iranges-2.14.12-r351h470a237_0.tar.bz2
+md5         : 122f9bf65025dc0aceca3aec7335ea7a
+timestamp   : 2018-10-12 13:05:24 UTC
+dependencies: 
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+  - libgcc-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
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+bioconductor-iranges 2.16.0 r351h14c3975_0
+------------------------------------------
+file name   : bioconductor-iranges-2.16.0-r351h14c3975_0.tar.bz2
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+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-iranges 2.18.1 r36h516909a_0
+-----------------------------------------
+file name   : bioconductor-iranges-2.18.1-r36h516909a_0.tar.bz2
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+md5         : d698f0be6a21bb48be249e400d7a7c1b
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+  - libgcc-ng >=7.3.0
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+bioconductor-iranges 2.18.2 r36h516909a_0
+-----------------------------------------
+file name   : bioconductor-iranges-2.18.2-r36h516909a_0.tar.bz2
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+-----------------------------------------
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BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-jazzpanda.manual_bundle.txt

@@ -0,0 +1,51 @@
+# Tool: bioconductor-jazzpanda
+software_name: bioconductor-jazzpanda
+tier: T1
+domain: spatial_transcriptomics
+downloads: 30
+summary: Finding spatially relevant marker genes in image based spatial transcriptomics data
+description: This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, r-base >=4.5,<4.6.0a0, r-caret, r-doparallel, r-dplyr, r-foreach, r-glmnet, r-magrittr, r-spatstat.geom
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/jazzPanda.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/jazzPanda.html
+Bioconductor - jazzPanda Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages jazzPanda jazzPanda This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see jazzPanda . Finding spatially relevant marker genes in image based spatial transcriptomics data DOI: 10.18129/B9.bioc.jazzPanda Bioconductor version: 3.22 This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise. Author: Melody Jin [aut, cre] ORCID: 0000-0002-2222-0958 Maintainer: Melody Jin &#x3c;&#x6a;&#x69;&#x6e;&#x2e;&#x6d;&#x20;&#x61;&#x74;&#x20;&#x77;&#x65;&#x68;&#x69;&#x2e;&#x65;&#x64;&#x75;&#x2e;&#x61;&#x75;&#x3e; Citation (from within R, enter citation("jazzPanda") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("jazzPanda") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("jazzPanda") jazzPanda example HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DifferentialExpression , GeneExpression , Software , Spatial , StatisticalMethod , Transcriptomics Version 1.2.0 In Bioconductor since BioC 3.21 (R-4.5) (1 year) License GPL-3 Depends R (>= 4.5.0) Imports spatstat.geom , dplyr , glmnet , caret , foreach , stats, magrittr , doParallel , BiocParallel , methods, BumpyMatrix , SpatialExperiment System Requirements URL https://github.com/phipsonlab/jazzPanda https://bhuvad.github.io/jazzPanda/ Bug Reports https://github.com/phipsonlab/jazzPanda/issues See More Suggests BiocStyle , knitr , rmarkdown , spatstat , Seurat , statmod , corrplot , ggplot2 , ggraph , ggrepel , gridExtra , reshape2 , igraph , jsonlite , vdiffr , patchwork , ggpubr , tidyr , SpatialFeatureExperiment , ExperimentHub , TENxXeniumData , SingleCellExperiment , SFEData , Matrix , data.table , scran , scater , grid, GenomeInfoDb , testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package jazzPanda_1.2.0.tar.gz Windows Binary (x86_64) jazzPanda_1.2.0.zip macOS Binary (x86_64) jazzPanda_1.2.0.tgz macOS Binary (arm64) jazzPanda_1.2.0.tgz Source Repository git clone https://git.bioconductor.org/packages/jazzPanda Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/jazzPanda Bioc Package Browser https://code.bioconductor.org/browse/jazzPanda/ Package Short Url https://bioconductor.org/packages/jazzPanda/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-jazzpanda --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-jazzpanda 1.2.0 r45hdfd78af_0
+------------------------------------------
+file name   : bioconductor-jazzpanda-1.2.0-r45hdfd78af_0.conda
+name        : bioconductor-jazzpanda
+version     : 1.2.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 4.4 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-jazzpanda-1.2.0-r45hdfd78af_0.conda
+md5         : 077f10f80bd1f2144270676649abf15c
+timestamp   : 2026-03-01 16:22:32 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-bumpymatrix >=1.18.0,<1.19.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - r-base >=4.5,<4.6.0a0
+  - r-caret
+  - r-doparallel
+  - r-dplyr
+  - r-foreach
+  - r-glmnet
+  - r-magrittr
+  - r-spatstat.geom

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-matrixgenerics.manual_bundle.txt

@@ -0,0 +1,296 @@
+# Tool: bioconductor-matrixgenerics
+software_name: bioconductor-matrixgenerics
+tier: T1
+domain: t1_backfill_overall
+downloads: 1199955
+summary: S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
+description: S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.
+dependencies: r-base >=4.5,<4.6.0a0, r-matrixstats >=1.4.1
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.11/bioc/html/MatrixGenerics.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.11/bioc/html/MatrixGenerics.html
+Bioconductor - MatrixGenerics About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages MatrixGenerics MatrixGenerics This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MatrixGenerics . S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects DOI: 10.18129/B9.bioc.MatrixGenerics Bioconductor version: 3.11 S4 generic functions modeled after the 'matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities. Author: Constantin Ahlmann-Eltze [aut] , Peter Hickey [aut, cre] Maintainer: Peter Hickey &#x3c;&#x70;&#x65;&#x74;&#x65;&#x72;&#x2e;&#x68;&#x69;&#x63;&#x6b;&#x65;&#x79;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("MatrixGenerics") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MatrixGenerics") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.2 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License Artistic-2.0 Depends matrixStats (>= 0.56.0) Imports methods System Requirements URL https://github.com/Bioconductor/MatrixGenerics Bug Reports https://github.com/Bioconductor/MatrixGenerics/issues See More Suggests testthat (>= 2.1.0) Linking To Enhances Depends On Me Imports Me sparseMatrixStats Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MatrixGenerics_1.0.2.tar.gz Windows Binary MatrixGenerics_1.0.2.zip macOS 10.13 (High Sierra) MatrixGenerics_1.0.2.tgz Source Repository git clone https://git.bioconductor.org/packages/MatrixGenerics Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MatrixGenerics Bioc Package Browser https://code.bioconductor.org/browse/MatrixGenerics/ Package Short Url https://bioconductor.org/packages/MatrixGenerics/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-matrixgenerics --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-matrixgenerics 1.0.0 r36_0
+---------------------------------------
+file name   : bioconductor-matrixgenerics-1.0.0-r36_0.tar.bz2
+name        : bioconductor-matrixgenerics
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+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.0.0-r36_0.tar.bz2
+md5         : 9c736f84a2b80f14b1e458c577ff363f
+timestamp   : 2020-05-05 13:12:27 UTC
+dependencies: 
+  - r-base >=3.6,<3.7.0a0
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-matrixgenerics 1.0.0 r40_1
+---------------------------------------
+file name   : bioconductor-matrixgenerics-1.0.0-r40_1.tar.bz2
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.0.0-r40_1.tar.bz2
+md5         : 885ace9ec4669960523689e9a5a6a2ae
+timestamp   : 2020-05-09 16:22:42 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-matrixstats >=0.56.0
+
+
+bioconductor-matrixgenerics 1.2.0 r40_0
+---------------------------------------
+file name   : bioconductor-matrixgenerics-1.2.0-r40_0.tar.bz2
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+md5         : 3e4bbb486f11ca12b741b6f77e8e5dc7
+timestamp   : 2020-10-29 12:35:28 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-matrixstats >=0.57.0
+
+
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+-----------------------------------------------
+file name   : bioconductor-matrixgenerics-1.2.1-r40hdfd78af_0.tar.bz2
+name        : bioconductor-matrixgenerics
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+md5         : b22671384108edc71b35d5ab0cf31c08
+timestamp   : 2021-03-27 23:02:09 UTC
+dependencies: 
+  - r-base >=4.0,<4.1.0a0
+  - r-matrixstats >0.57.0
+
+
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+-----------------------------------------------
+file name   : bioconductor-matrixgenerics-1.4.0-r41hdfd78af_0.tar.bz2
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+md5         : eff7c55a3f0d916cf09fc7db0232b04c
+timestamp   : 2021-05-31 02:39:16 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-matrixstats >0.57.0
+
+
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+-----------------------------------------------
+file name   : bioconductor-matrixgenerics-1.6.0-r41hdfd78af_0.tar.bz2
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+md5         : 69613f3c312fb36021947f3359e89435
+timestamp   : 2021-11-01 16:32:48 UTC
+dependencies: 
+  - r-base >=4.1,<4.2.0a0
+  - r-matrixstats >=0.60.1
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+
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+------------------------------------------------
+file name   : bioconductor-matrixgenerics-1.10.0-r42hdfd78af_0.tar.bz2
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+timestamp   : 2022-11-03 07:31:14 UTC
+dependencies: 
+  - r-base >=4.2,<4.3.0a0
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+------------------------------------------------
+file name   : bioconductor-matrixgenerics-1.12.2-r43hdfd78af_0.tar.bz2
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+timestamp   : 2023-07-07 14:05:15 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+  - r-matrixstats >=1.0.0
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+------------------------------------------------
+file name   : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_0.tar.bz2
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+timestamp   : 2023-12-02 19:53:22 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+  - r-matrixstats >=1.0.0
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+------------------------------------------------
+file name   : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_1.tar.bz2
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+md5         : 820657575f114f4f80071bfb0c4a95b7
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+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+  - r-matrixstats >=1.0.0
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+
+bioconductor-matrixgenerics 1.14.0 r43hdfd78af_2
+------------------------------------------------
+file name   : bioconductor-matrixgenerics-1.14.0-r43hdfd78af_2.tar.bz2
+name        : bioconductor-matrixgenerics
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+build number: 2
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+license     : Artistic-2.0
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+timestamp   : 2024-05-03 07:00:59 UTC
+dependencies: 
+  - r-base >=4.3,<4.4.0a0
+  - r-matrixstats >=1.0.0
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+------------------------------------------------
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+timestamp   : 2024-05-03 12:11:07 UTC
+dependencies: 
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+------------------------------------------------
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+dependencies: 
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+  - r-matrixstats >=1.4.1
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+------------------------------------------------
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BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-merfishdata.manual_bundle.txt

@@ -0,0 +1,160 @@
+# Tool: bioconductor-merfishdata
+software_name: bioconductor-merfishdata
+tier: T1
+domain: spatial_transcriptomics
+downloads: 4053
+summary: Collection of public MERFISH datasets
+description: MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.
+dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-data-packages >=20260207, bioconductor-ebimage >=4.52.0,<4.53.0, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-hdf5array >=1.38.0,<1.39.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.16/data/experiment/html/MerfishData.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.16/data/experiment/html/MerfishData.html
+Bioconductor - MerfishData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Experiment Packages MerfishData MerfishData This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see MerfishData . Collection of public MERFISH datasets DOI: 10.18129/B9.bioc.MerfishData Bioconductor version: 3.16 MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis. Author: Ludwig Geistlinger [aut, cre] , Tyrone Lee [ctb], Helena Crowell [ctb] , Jeffrey Mofitt [aut], Robert Gentleman [aut] Maintainer: Ludwig Geistlinger &#x3c;&#x6c;&#x75;&#x64;&#x77;&#x69;&#x67;&#x5f;&#x67;&#x65;&#x69;&#x73;&#x74;&#x6c;&#x69;&#x6e;&#x67;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x68;&#x6d;&#x73;&#x2e;&#x68;&#x61;&#x72;&#x76;&#x61;&#x72;&#x64;&#x2e;&#x65;&#x64;&#x75;&#x3e; Citation (from within R, enter citation("MerfishData") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MerfishData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("MerfishData") Mouse hypothalamus HTML R Script Mouse ileum HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , HighThroughputImagingData , Mus_musculus_Data , SingleCellData , SpatialData Version 1.0.0 License Artistic-2.0 Depends R (>= 4.2.0), EBImage , SpatialExperiment Imports grDevices, AnnotationHub , BumpyMatrix , ExperimentHub , S4Vectors , SummarizedExperiment System Requirements URL https://github.com/ccb-hms/MerfishData Bug Reports https://github.com/ccb-hms/MerfishData/issues See More Suggests grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle , ExperimentHubData Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MerfishData_1.0.0.tar.gz Windows Binary macOS Binary (x86_64) macOS Binary (arm64) Source Repository git clone https://git.bioconductor.org/packages/MerfishData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MerfishData Package Short Url https://bioconductor.org/packages/MerfishData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-merfishdata --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / done
+bioconductor-merfishdata 1.0.0 r42hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-merfishdata-1.0.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-merfishdata
+version     : 1.0.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 10 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.0.0-r42hdfd78af_0.tar.bz2
+md5         : 47b6c3e21bde878d95520b7edabab71b
+timestamp   : 2022-11-09 02:26:57 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.6.0,<3.7.0
+  - bioconductor-bumpymatrix >=1.6.0,<1.7.0
+  - bioconductor-data-packages >=20221108
+  - bioconductor-ebimage >=4.40.0,<4.41.0
+  - bioconductor-experimenthub >=2.6.0,<2.7.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - bioconductor-spatialexperiment >=1.8.0,<1.9.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - curl
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-merfishdata 1.2.0 r43hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-merfishdata-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-merfishdata
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 10 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : 5e8c9c555435a2cd7ad3ab0f3d64d64f
+timestamp   : 2023-07-16 14:28:49 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.8.0,<3.9.0
+  - bioconductor-bumpymatrix >=1.8.0,<1.9.0
+  - bioconductor-data-packages >=20230706
+  - bioconductor-ebimage >=4.42.0,<4.43.0
+  - bioconductor-experimenthub >=2.8.0,<2.9.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-merfishdata 1.4.1 r43hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-merfishdata-1.4.1-r43hdfd78af_0.tar.bz2
+name        : bioconductor-merfishdata
+version     : 1.4.1
+build       : r43hdfd78af_0
+build number: 0
+size        : 10 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.4.1-r43hdfd78af_0.tar.bz2
+md5         : 33391f6d7214415a92549e52f5009a7c
+timestamp   : 2023-12-08 14:10:13 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.10.0,<3.11.0
+  - bioconductor-bumpymatrix >=1.10.0,<1.11.0
+  - bioconductor-data-packages >=20231203
+  - bioconductor-ebimage >=4.44.0,<4.45.0
+  - bioconductor-experimenthub >=2.10.0,<2.11.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-merfishdata 1.8.0 r44hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-merfishdata-1.8.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-merfishdata
+version     : 1.8.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 10 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.8.0-r44hdfd78af_0.tar.bz2
+md5         : 563deedc848beffd0feae58f95ca0a88
+timestamp   : 2025-01-05 01:57:39 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.14.0,<3.15.0
+  - bioconductor-bumpymatrix >=1.14.0,<1.15.0
+  - bioconductor-data-packages >=20250104
+  - bioconductor-ebimage >=4.48.0,<4.49.0
+  - bioconductor-experimenthub >=2.14.0,<2.15.0
+  - bioconductor-hdf5array >=1.34.0,<1.35.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-singlecellexperiment >=1.28.0,<1.29.0
+  - bioconductor-spatialexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - curl
+  - r-base >=4.4,<4.5.0a0
+
+
+bioconductor-merfishdata 1.12.0 r45hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-merfishdata-1.12.0-r45hdfd78af_0.conda
+name        : bioconductor-merfishdata
+version     : 1.12.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 12 KB
+license     : Artistic-2.0
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-merfishdata-1.12.0-r45hdfd78af_0.conda
+md5         : a3b24a43bf4769fd542cb9f3bf8c8447
+timestamp   : 2026-03-01 22:07:50 UTC
+dependencies: 
+  - bioconductor-annotationhub >=4.0.0,<4.1.0
+  - bioconductor-bumpymatrix >=1.18.0,<1.19.0
+  - bioconductor-data-packages >=20260207
+  - bioconductor-ebimage >=4.52.0,<4.53.0
+  - bioconductor-experimenthub >=3.0.0,<3.1.0
+  - bioconductor-hdf5array >=1.38.0,<1.39.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - curl
+  - r-base >=4.5,<4.6.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-mousegastrulationdata.manual_bundle.txt

@@ -0,0 +1,294 @@
+# Tool: bioconductor-mousegastrulationdata
+software_name: bioconductor-mousegastrulationdata
+tier: T1
+domain: spatial_transcriptomics
+downloads: 18021
+summary: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis
+description: Provides processed and raw count data for single-cell RNA sequencing, single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis.
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-bumpymatrix >=1.18.0,<1.19.0, bioconductor-data-packages >=20260207, bioconductor-experimenthub >=3.0.0,<3.1.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-spatialexperiment >=1.20.0,<1.21.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.10/data/experiment/html/MouseGastrulationData.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.10/data/experiment/html/MouseGastrulationData.html
+Bioconductor - MouseGastrulationData About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.10 Experiment Packages MouseGastrulationData MouseGastrulationData This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see MouseGastrulationData . Single-Cell Transcriptomics Data across Mouse Gastrulation and Early Organogenesis DOI: 10.18129/B9.bioc.MouseGastrulationData Bioconductor version: 3.10 Provides processed and raw count matrices for single-cell RNA sequencing data from a timecourse of mouse gastrulation and early organogenesis. Author: Jonathan Griffiths [aut, cre], Aaron Lun [aut] Maintainer: Jonathan Griffiths &#x3c;&#x6a;&#x6f;&#x6e;&#x61;&#x74;&#x68;&#x61;&#x6e;&#x2e;&#x67;&#x72;&#x69;&#x66;&#x66;&#x69;&#x74;&#x68;&#x73;&#x2e;&#x39;&#x34;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("MouseGastrulationData") ): Installation To install this package, start R (version "3.6") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MouseGastrulationData") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("MouseGastrulationData") Available datasets HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews ExperimentData , ExperimentHub , ExpressionData , RNASeqData , SequencingData , SingleCellData Version 1.0.0 License GPL-3 Depends R (>= 3.6.0), SingleCellExperiment Imports methods, ExperimentHub , BiocGenerics , S4Vectors System Requirements URL https://github.com/MarioniLab/MouseGastrulationData Bug Reports https://github.com/MarioniLab/MouseGastrulationData/issues See More Suggests BiocStyle , knitr, rmarkdown Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package MouseGastrulationData_1.0.0.tar.gz Windows Binary Mac OS X 10.11 (El Capitan) Source Repository git clone https://git.bioconductor.org/packages/MouseGastrulationData Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MouseGastrulationData Package Short Url https://bioconductor.org/packages/MouseGastrulationData/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-mousegastrulationdata --info
+[rc=0]
+2 channel Terms of 
+Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-mousegastrulationdata 1.0.0 r36_0
+----------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.0.0-r36_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.0.0
+build       : r36_0
+build number: 0
+size        : 18 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.0.0-r36_0.tar.bz2
+md5         : f28ab3665718590b46d1567a0271a69a
+timestamp   : 2019-11-07 02:48:13 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.32.0,<0.33.0
+  - bioconductor-experimenthub >=1.12.0,<1.13.0
+  - bioconductor-s4vectors >=0.24.0,<0.25.0
+  - bioconductor-singlecellexperiment >=1.8.0,<1.9.0
+  - curl
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-mousegastrulationdata 1.2.0 r40_0
+----------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.2.0-r40_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.2.0
+build       : r40_0
+build number: 0
+size        : 18 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.2.0-r40_0.tar.bz2
+md5         : e3ed0972455ecbd35a81a209d32fff1f
+timestamp   : 2020-05-10 22:23:14 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.34.0,<0.35.0
+  - bioconductor-experimenthub >=1.14.0,<1.15.0
+  - bioconductor-s4vectors >=0.26.0,<0.27.0
+  - bioconductor-singlecellexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.18.0,<1.19.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-mousegastrulationdata 1.4.0 r40_0
+----------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.4.0-r40_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.4.0
+build       : r40_0
+build number: 0
+size        : 19 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.4.0-r40_0.tar.bz2
+md5         : 17cff8fb93d3c5c99081a3bd419816ec
+timestamp   : 2020-11-02 12:41:16 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.36.0,<0.37.0
+  - bioconductor-experimenthub >=1.16.0,<1.17.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - bioconductor-singlecellexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.20.0,<1.21.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-mousegastrulationdata 1.4.0 r40hdfd78af_1
+------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.4.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.4.0
+build       : r40hdfd78af_1
+build number: 1
+size        : 19 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.4.0-r40hdfd78af_1.tar.bz2
+md5         : e069cdc9e039eb58efcb0526fea2d772
+timestamp   : 2021-03-31 12:51:39 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.36.0,<0.37.0
+  - bioconductor-experimenthub >=1.16.0,<1.17.0
+  - bioconductor-s4vectors >=0.28.0,<0.29.0
+  - bioconductor-singlecellexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.20.0,<1.21.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-mousegastrulationdata 1.6.0 r41hdfd78af_0
+------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.6.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.6.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.6.0-r41hdfd78af_0.tar.bz2
+md5         : bb2195352c48645676ae08e9d239010c
+timestamp   : 2021-06-07 09:30:31 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.38.0,<0.39.0
+  - bioconductor-bumpymatrix >=1.0.0,<1.1.0
+  - bioconductor-experimenthub >=2.0.0,<2.1.0
+  - bioconductor-s4vectors >=0.30.0,<0.31.0
+  - bioconductor-singlecellexperiment >=1.14.0,<1.15.0
+  - bioconductor-spatialexperiment >=1.2.0,<1.3.0
+  - bioconductor-summarizedexperiment >=1.22.0,<1.23.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-mousegastrulationdata 1.8.0 r41hdfd78af_0
+------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.8.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_0.tar.bz2
+md5         : 5dcf75d042e10d8372d330e00c15abea
+timestamp   : 2021-11-08 04:55:56 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.40.0,<0.41.0
+  - bioconductor-bumpymatrix >=1.2.0,<1.3.0
+  - bioconductor-experimenthub >=2.2.0,<2.3.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - bioconductor-spatialexperiment >=1.4.0,<1.5.0
+  - bioconductor-summarizedexperiment >=1.24.0,<1.25.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-mousegastrulationdata 1.8.0 r41hdfd78af_1
+------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_1.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.8.0
+build       : r41hdfd78af_1
+build number: 1
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.8.0-r41hdfd78af_1.tar.bz2
+md5         : 7c6f0d5b88ec0134dd25c24e48f2d6af
+timestamp   : 2022-08-30 03:56:41 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.40.0,<0.41.0
+  - bioconductor-bumpymatrix >=1.2.0,<1.3.0
+  - bioconductor-experimenthub >=2.2.0,<2.3.0
+  - bioconductor-s4vectors >=0.32.0,<0.33.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - bioconductor-spatialexperiment >=1.4.0,<1.5.0
+  - bioconductor-summarizedexperiment >=1.24.0,<1.25.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-mousegastrulationdata 1.12.0 r42hdfd78af_0
+-------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.12.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.12.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 20 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.12.0-r42hdfd78af_0.tar.bz2
+md5         : 98617c9f9f039802012d3bc8630d5197
+timestamp   : 2022-11-09 02:11:10 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.44.0,<0.45.0
+  - bioconductor-bumpymatrix >=1.6.0,<1.7.0
+  - bioconductor-data-packages >=20221108
+  - bioconductor-experimenthub >=2.6.0,<2.7.0
+  - bioconductor-s4vectors >=0.36.0,<0.37.0
+  - bioconductor-singlecellexperiment >=1.20.0,<1.21.0
+  - bioconductor-spatialexperiment >=1.8.0,<1.9.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - curl
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-mousegastrulationdata 1.14.0 r43hdfd78af_0
+-------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.14.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.14.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 21 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.14.0-r43hdfd78af_0.tar.bz2
+md5         : 27931785fb1036ccb5eddd19d0e8217a
+timestamp   : 2023-07-16 14:12:32 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.46.0,<0.47.0
+  - bioconductor-bumpymatrix >=1.8.0,<1.9.0
+  - bioconductor-data-packages >=20230706
+  - bioconductor-experimenthub >=2.8.0,<2.9.0
+  - bioconductor-s4vectors >=0.38.0,<0.39.0
+  - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-mousegastrulationdata 1.16.0 r43hdfd78af_0
+-------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.16.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-mousegastrulationdata
+version     : 1.16.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 21 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.16.0-r43hdfd78af_0.tar.bz2
+md5         : 652738b1e9f0b9e7fab04c2a6337936b
+timestamp   : 2023-12-08 11:32:02 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.48.0,<0.49.0
+  - bioconductor-bumpymatrix >=1.10.0,<1.11.0
+  - bioconductor-data-packages >=20231203
+  - bioconductor-experimenthub >=2.10.0,<2.11.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - curl
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-mousegastrulationdata 1.24.0 r45hdfd78af_0
+-------------------------------------------------------
+file name   : bioconductor-mousegastrulationdata-1.24.0-r45hdfd78af_0.conda
+name        : bioconductor-mousegastrulationdata
+version     : 1.24.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 23 KB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-mousegastrulationdata-1.24.0-r45hdfd78af_0.conda
+md5         : 1b201133e83f2436d523e28d82b8e54e
+timestamp   : 2026-03-01 23:38:41 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.56.0,<0.57.0
+  - bioconductor-bumpymatrix >=1.18.0,<1.19.0
+  - bioconductor-data-packages >=20260207
+  - bioconductor-experimenthub >=3.0.0,<3.1.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-spatialexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - curl
+  - r-base >=4.5,<4.6.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.ce.eg.db.manual_bundle.txt

@@ -0,0 +1,397 @@
+# Tool: bioconductor-org.ce.eg.db
+software_name: bioconductor-org.ce.eg.db
+tier: T1
+domain: t1_backfill_overall
+downloads: 116707
+summary: Genome wide annotation for Worm
+description: Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.
+dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/data/annotation/html/org.Ce.eg.db.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/data/annotation/html/org.Ce.eg.db.html
+Bioconductor - org.Ce.eg.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages org.Ce.eg.db org.Ce.eg.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see org.Ce.eg.db . Genome wide annotation for Worm DOI: 10.18129/B9.bioc.org.Ce.eg.db Bioconductor version: 3.22 Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("org.Ce.eg.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("org.Ce.eg.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Caenorhabditis_elegans , OrgDb Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI , annotate , RUnit Linking To Enhances Depends On Me celegans.db Imports Me CoSIA Suggests Me ChIPpeakAnno , geneXtendeR , goatea , goSorensen , multiGSEA , NetSAM , rrvgo , scQTLtools , goat Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package org.Ce.eg.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/org.Ce.eg.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-org.ce.eg.db --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-org.ce.eg.db 3.2.3 0
+---------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-0.tar.bz2
+name        : bioconductor-org.ce.eg.db
+version     : 3.2.3
+build       : 0
+build number: 0
+size        : 13.3 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-0.tar.bz2
+md5         : 74af90e36e8d9f6acf0207c04ea40485
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r >=2.7.0
+
+
+bioconductor-org.ce.eg.db 3.2.3 r3.3.1_0
+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r3.3.1_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build       : r3.3.1_0
+build number: 0
+size        : 13.3 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.3.1_0.tar.bz2
+md5         : ec2f9f9497684d0e75e1de340b1be402
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r 3.3.1*
+
+
+bioconductor-org.ce.eg.db 3.2.3 r3.3.2_0
+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r3.3.2_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build       : r3.3.2_0
+build number: 0
+size        : 13.3 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.3.2_0.tar.bz2
+md5         : 25098bb2b119cb08c893282fd277c40a
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r-base 3.3.2*
+
+
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+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r3.4.1_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.4.1_0.tar.bz2
+md5         : 5f04213cdf80a155e6199b6e0fd3c78a
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r-base 3.4.1*
+
+
+bioconductor-org.ce.eg.db 3.2.3 r3.4.1_1
+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r3.4.1_1.tar.bz2
+name        : bioconductor-org.ce.eg.db
+version     : 3.2.3
+build       : r3.4.1_1
+build number: 1
+size        : 5 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r3.4.1_1.tar.bz2
+md5         : 2b496e033950467b43eef5c50e5dd8c1
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r-base 3.4.1*
+  - wget
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r341_2.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build number: 2
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+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r341_2.tar.bz2
+md5         : 289c92ad717298f79495846d97e44e6b
+timestamp   : 2018-10-18 21:21:33 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r-base >=3.4.1,<3.4.2.0a0
+  - wget
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.2.3-r351_2.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build       : r351_2
+build number: 2
+size        : 6 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.2.3-r351_2.tar.bz2
+md5         : bfc833763f6cb41b554863a8a64749d1
+timestamp   : 2018-10-18 21:19:57 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.31.19
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.4.1 r3.4.1_0
+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.4.1-r3.4.1_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r3.4.1_0.tar.bz2
+md5         : 12eef1df469dec1dcbfa1a0a3bd5ac1d
+dependencies: 
+  - bioconductor-annotationdbi >=1.37.4
+  - r-base 3.4.1*
+  - wget
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.4.1-r341_1.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build number: 1
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+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r341_1.tar.bz2
+md5         : 1cb6e4d2f1c8243f4321779795490505
+timestamp   : 2018-10-18 21:46:53 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.37.4
+  - r-base >=3.4.1,<3.4.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.4.1 r351_1
+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.4.1-r351_1.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+build number: 1
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+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.4.1-r351_1.tar.bz2
+md5         : 09e54fc462f15121a709e64ac9d76666
+timestamp   : 2018-10-18 21:45:10 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.37.4
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.5.0 r3.4.1_0
+----------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.5.0-r3.4.1_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.5.0-r3.4.1_0.tar.bz2
+md5         : 8ea7e90fc2d62f52bb7ec02a86cac5d6
+dependencies: 
+  - bioconductor-annotationdbi >=1.39.3
+  - r-base 3.4.1*
+  - wget
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.6.0-r341_0.tar.bz2
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.6.0-r341_0.tar.bz2
+md5         : bcceb95ede91f8605e5c4117ea825789
+timestamp   : 2018-10-18 21:32:05 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - r-base >=3.4.1,<3.4.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.6.0 r351_0
+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.6.0-r351_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-org.ce.eg.db-3.6.0-r351_0.tar.bz2
+md5         : fd6560c9aaf4ff6a4d2778ee723ff752
+timestamp   : 2018-10-18 21:33:44 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.42.1,<1.44.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.7.0 r351_0
+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.7.0-r351_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.7.0-r351_0.tar.bz2
+md5         : 51362f3c2da134b6a6bf7ec36aadca95
+timestamp   : 2018-12-26 20:07:44 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.44.0,<1.45.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - wget
+
+
+bioconductor-org.ce.eg.db 3.8.2 r36_1
+-------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.8.2-r36_1.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.8.2-r36_1.tar.bz2
+md5         : a979ceae50bac4b1a920ffe35a09b6e7
+timestamp   : 2019-08-06 09:12:51 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.46.0,<1.47.0
+  - curl
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-org.ce.eg.db 3.10.0 r36_0
+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.10.0-r36_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+md5         : 7cff302b5df5f3b1968ed4197f4723ea
+timestamp   : 2019-11-02 22:12:21 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.48.0,<1.49.0
+  - curl
+  - r-base >=3.6,<3.7.0a0
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.11.1-r40_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-org.ce.eg.db-3.11.1-r40_0.tar.bz2
+md5         : 26ea75ba02bae36c5ed5eb2e6585fe03
+timestamp   : 2020-05-10 13:24:22 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.50.0,<1.51.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
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+--------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.12.0-r40_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+md5         : 3325ccda939368bb21bfb372bdde7d44
+timestamp   : 2020-10-30 09:01:03 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-org.ce.eg.db 3.12.0 r40hdfd78af_1
+----------------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.12.0-r40hdfd78af_1.tar.bz2
+name        : bioconductor-org.ce.eg.db
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+md5         : 08363c82c33e616fe18ac2aa1a16ca8a
+timestamp   : 2021-03-29 22:05:28 UTC
+dependencies: 
+  - bioconductor-annotationdbi >=1.52.0,<1.53.0
+  - curl
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-org.ce.eg.db 3.13.0 r41hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-org.ce.eg.db-3.13.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-org.ce.eg.db
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BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-org.hs.eg.db.manual_bundle.txt

@@ -0,0 +1,406 @@
+# Tool: bioconductor-org.hs.eg.db
+software_name: bioconductor-org.hs.eg.db
+tier: T1
+domain: t1_backfill_overall
+downloads: 163395
+summary: Genome wide annotation for Human
+description: Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.
+dependencies: bioconductor-annotationdbi >=1.72.0,<1.73.0, bioconductor-data-packages >=20260207, curl, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/data/annotation/html/org.Hs.eg.db.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/data/annotation/html/org.Hs.eg.db.html
+Bioconductor - org.Hs.eg.db Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Annotation Packages org.Hs.eg.db org.Hs.eg.db This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see org.Hs.eg.db . Genome wide annotation for Human DOI: 10.18129/B9.bioc.org.Hs.eg.db Bioconductor version: 3.22 Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers. Author: Marc Carlson Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("org.Hs.eg.db") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("org.Hs.eg.db") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews AnnotationData , Homo_sapiens , OrgDb , humanLLMappings Version 3.22.0 License Artistic-2.0 Depends R (>= 2.7.0), methods, AnnotationDbi (>= 1.71.1) Imports System Requirements URL See More Suggests DBI , annotate , RUnit Linking To Enhances Depends On Me CoCiteStats , GSReg , KEGGlincs , signatureSearch , tRanslatome , clariomdhumanprobeset.db , clariomdhumantranscriptcluster.db , clariomshumanhttranscriptcluster.db , clariomshumantranscriptcluster.db , FDb.InfiniumMethylation.hg18 , FDb.InfiniumMethylation.hg19 , GGHumanMethCancerPanelv1.db , h10kcod.db , h20kcod.db , hcg110.db , hgfocus.db , hgu133a.db , hgu133a2.db , hgu133b.db , hgu133plus2.db , hgu219.db , hgu95a.db , hgu95av2.db , hgu95b.db , hgu95c.db , hgu95d.db , hgu95e.db , hguatlas13k.db , hgubeta7.db , hguDKFZ31.db , hgug4100a.db , hgug4101a.db , hgug4110b.db , hgug4111a.db , hgug4112a.db , hgug4845a.db , hguqiagenv3.db , hi16cod.db , Homo.sapiens , hs25kresogen.db , Hs6UG171.db , HsAgilentDesign026652.db , hta20probeset.db , hta20transcriptcluster.db , hthgu133a.db , hthgu133b.db , hthgu133plusa.db , hthgu133plusb.db , hthgu133pluspm.db , hu35ksuba.db , hu35ksubb.db , hu35ksubc.db , hu35ksubd.db , hu6800.db , huex10stprobeset.db , huex10sttranscriptcluster.db , hugene10stprobeset.db , hugene10sttranscriptcluster.db , hugene11stprobeset.db , hugene11sttranscriptcluster.db , hugene20stprobeset.db , hugene20sttranscriptcluster.db , hugene21stprobeset.db , hugene21sttranscriptcluster.db , HuO22.db , hwgcod.db , IlluminaHumanMethylation27k.db , illuminaHumanv1.db , illuminaHumanv2.db , illuminaHumanv2BeadID.db , illuminaHumanv3.db , illuminaHumanv4.db , illuminaHumanWGDASLv3.db , illuminaHumanWGDASLv4.db , JazaeriMetaData.db , LAPOINTE.db , lumiHumanAll.db , Norway981.db , nugohs1a520180.db , OperonHumanV3.db , PartheenMetaData.db , pedbarrayv10.db , pedbarrayv9.db , POCRCannotation.db , Roberts2005Annotation.db , SHDZ.db , u133x3p.db , annotation , rnaseqGene , variants , OSCA.workflows Imports Me APL , artMS , attract , bioCancer , BioNAR , CaMutQC , CBNplot , cellity , chimeraviz , chipenrich , consensusDE , consICA , CoSIA , debrowser , DegCre , EasyCellType , EGSEA , famat , funOmics , GDCRNATools , geneAttribution , GmicR , GOpro , goSorensen , mastR , MCbiclust , MetaboSignal , methylGSA , mirIntegrator , miRLAB , miRSM , miRspongeR , missMethyl , mitology , Moonlight2R , MOSClip , mslp , OutSplice , PanomiR , pathview , REMP , rGREAT , rgsepd , RNAAgeCalc , rTRMui , scafari , scPipe , signifinder , SMITE , sSNAPPY , SubCellBarCode , SVMDO , TFEA.ChIP , TFutils , uncoverappLib , GenomicState , SomaScan.db , msigdb , recountWorkflow Suggests Me AllelicImbalance , annotate , AnnotationDbi , AnnotationFilter , AnnotationForge , annotatr , appreci8R , ASURAT , autonomics , BioCor , BiocSet , BioQC , borealis , bumphunter , categoryCompare , CeTF , ChIPpeakAnno , ChIPseeker , clusterProfiler , cnvGSA , CNVRanger , CRISPRseek , DeeDeeExperiment , derfinderPlot , dmGsea , dmrseq , DOSE , edgeR , EnhancedVolcano , enhancerHomologSearch , enrichplot , EpiCompare , EpiMix , esATAC , FELLA , fishpond , FRASER , GA4GHclient , GA4GHshiny , gage , gCrisprTools , GeDi , GeneNetworkBuilder , GeneTonic , geneXtendeR , GenomicFeatures , GenomicInteractionNodes , geomeTriD , GeoTcgaData , gg4way , globaltest , gmapR , goatea , goProfiles , GOSemSim , goseq , GOstats , GRaNIE , graphite , groHMM , GSAR , GSEABase , GSVA , GUIDEseq , gwascat , hpar , ideal , iNETgrate , InteractiveComplexHeatmap , iSEEde , iSEEpathways , iSEEu , karyoploteR , KEGGgraph , limma , linkSet , MesKit , MIRit , miRNAtap , MLP , mogsa , mosdef , multiGSEA , NanoMethViz , NetActivity , NetSAM , netZooR , ontoProc , oppar , Organism.dplyr , OUTRIDER , pageRank , pathlinkR , pcaExplorer , PCAtools , phantasus , Pigengene , plotgardener , ProteoDisco , PureCN , quantiseqr , R3CPET , ramr , ReactomePA , recount , RFLOMICS , rigvf , RnBeads , rrvgo , RTopper , rtracklayer , rTRM , scde , scFeatures , scGPS , scGraphVerse , scmeth , scQTLtools , simona , SingleCellAlleleExperiment , spatialHeatmap , SPICEY , svaRetro , TCGAutils , tenXplore , tidybulk , trackViewer , tricycle , Ularcirc , UMI4Cats , VariantFiltering , VariantTools , vissE , wiggleplotr , BloodCancerMultiOmics2017 , chipenrich.data , prostateCancerTaylor , RforProteomics , ExpHunterSuite , BaseSet , conos , convertid , coreheat , DIscBIO , driveR , easyEWAS , easylabel , goat , ivolcano , kernscr , lisat , metaMA , netgsa , pagoda2 , PANACEA , pathfindR , PathwayVote , pQTLdata , protr , RCPA , rliger , scPairs , SCpubr , SEMgraph , SurprisalAnalysis , WayFindR , XYomics Links To Me Package Archives Follow Installation instructions to use this package in your R session. Source Package org.Hs.eg.db_3.22.0.tar.gz Windows Binary (x86_64) macOS Binary (x86_64) macOS Binary (arm64) Package Short Url https://bioconductor.org/packages/org.Hs.eg.db/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
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+  - bioconductor-annotationdbi >=1.54.0,<1.55.0
+  - curl
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-org.hs.eg.db 3.14.0 r41hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-org.hs.eg.db-3.14.0-r41hdfd78af_0.tar.bz2
+name

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rbgl.manual_bundle.txt

@@ -0,0 +1,421 @@
+# Tool: bioconductor-rbgl
+software_name: bioconductor-rbgl
+tier: T1
+domain: t1_backfill_overall
+downloads: 123508
+summary: An interface to the BOOST graph library
+description: A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.
+dependencies: bioconductor-graph >=1.88.0,<1.89.0, bioconductor-graph >=1.88.1,<1.89.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-bh
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/RBGL.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/RBGL.html
+Bioconductor - RBGL Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages RBGL RBGL This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see RBGL . An interface to the BOOST graph library DOI: 10.18129/B9.bioc.RBGL Bioconductor version: 3.22 A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. Author: Vince Carey [aut], Li Long [aut], R. Gentleman [aut], Emmanuel Taiwo [ctb] (Converted RBGL vignette from Sweave to RMarkdown / HTML.), Bioconductor Package Maintainer [cre] Maintainer: Bioconductor Package Maintainer &#x3c;&#x6d;&#x61;&#x69;&#x6e;&#x74;&#x61;&#x69;&#x6e;&#x65;&#x72;&#x20;&#x61;&#x74;&#x20;&#x62;&#x69;&#x6f;&#x63;&#x6f;&#x6e;&#x64;&#x75;&#x63;&#x74;&#x6f;&#x72;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("RBGL") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RBGL") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("RBGL") RBGL Overview HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GraphAndNetwork , Network , Software Version 1.86.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (&gt; 21 years) License Artistic-2.0 Depends graph , methods Imports methods System Requirements URL http://www.bioconductor.org See More Suggests Rgraphviz , XML , RUnit , BiocGenerics , BiocStyle , knitr Linking To BH Enhances Depends On Me apComplex , BioNet , CellNOptR , fgga , PerfMeas Imports Me BiocPkgTools , biocViews , CAMERA , Category , ChIPpeakAnno , CHRONOS , CytoML , DEGraph , DEsubs , EventPointer , flowWorkspace , GenomicInteractionNodes , GOstats , NCIgraph , ontoProc , openCyto , OrganismDbi , Streamer , VariantFiltering , BiDAG , clustNet , eff2 , micd , pcalg , rags2ridges , RANKS , SEMgraph , SID Suggests Me DEGraph , G4SNVHunter , GeneNetworkBuilder , graph , gwascat , KEGGgraph , rBiopaxParser , VariantTools , yeastExpData , archeofrag , maGUI Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package RBGL_1.86.0.tar.gz Windows Binary (x86_64) RBGL_1.86.0.zip macOS Binary (x86_64) RBGL_1.86.0.tgz macOS Binary (arm64) RBGL_1.86.0.tgz Source Repository git clone https://git.bioconductor.org/packages/RBGL Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RBGL Bioc Package Browser https://code.bioconductor.org/browse/RBGL/ Package Short Url https://bioconductor.org/packages/RBGL/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-rbgl --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-rbgl 1.46.0 r3.2.2_0
+---------------------------------
+file name   : bioconductor-rbgl-1.46.0-r3.2.2_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.46.0
+build       : r3.2.2_0
+build number: 0
+size        : 1.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.2.2_0.tar.bz2
+md5         : bd95d054b992b7271898a7345553e01b
+dependencies: 
+  - bioconductor-graph
+  - r 3.2.2*
+
+
+bioconductor-rbgl 1.46.0 r3.2.2_1
+---------------------------------
+file name   : bioconductor-rbgl-1.46.0-r3.2.2_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.46.0
+build       : r3.2.2_1
+build number: 1
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.2.2_1.tar.bz2
+md5         : 9d93edcb3f2629ad9d7b37e51e21dabc
+dependencies: 
+  - bioconductor-graph
+  - r 3.2.2*
+
+
+bioconductor-rbgl 1.46.0 r3.3.1_1
+---------------------------------
+file name   : bioconductor-rbgl-1.46.0-r3.3.1_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.46.0
+build       : r3.3.1_1
+build number: 1
+size        : 1.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.46.0-r3.3.1_1.tar.bz2
+md5         : 84e6d3d980c08be799280a2997290888
+dependencies: 
+  - bioconductor-graph
+  - r 3.3.1*
+
+
+bioconductor-rbgl 1.48.1 r3.3.1_1
+---------------------------------
+file name   : bioconductor-rbgl-1.48.1-r3.3.1_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.48.1
+build       : r3.3.1_1
+build number: 1
+size        : 1.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.3.1_1.tar.bz2
+md5         : 3576e173b5433d3f290e13186ef0a60d
+dependencies: 
+  - bioconductor-graph
+  - r 3.3.1*
+
+
+bioconductor-rbgl 1.48.1 r3.3.2_1
+---------------------------------
+file name   : bioconductor-rbgl-1.48.1-r3.3.2_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.48.1
+build       : r3.3.2_1
+build number: 1
+size        : 1.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.3.2_1.tar.bz2
+md5         : db0b971d45accd178b1caab311377d25
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.3.2*
+
+
+bioconductor-rbgl 1.48.1 r3.4.1_1
+---------------------------------
+file name   : bioconductor-rbgl-1.48.1-r3.4.1_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.48.1
+build       : r3.4.1_1
+build number: 1
+size        : 1.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.48.1-r3.4.1_1.tar.bz2
+md5         : 1fc8d27965f10f1628a74256a799418e
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.4.1*
+
+
+bioconductor-rbgl 1.52.0 r3.4.1_0
+---------------------------------
+file name   : bioconductor-rbgl-1.52.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.52.0
+build       : r3.4.1_0
+build number: 0
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.52.0-r3.4.1_0.tar.bz2
+md5         : 09d9730486717d719ccf19bd1a7bb11e
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.4.1*
+
+
+bioconductor-rbgl 1.54.0 r3.4.1_0
+---------------------------------
+file name   : bioconductor-rbgl-1.54.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.54.0
+build       : r3.4.1_0
+build number: 0
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.54.0-r3.4.1_0.tar.bz2
+md5         : 08ce664aa302adcb92df73e232a727aa
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.4.1*
+
+
+bioconductor-rbgl 1.56.0 r341hfc679d8_0
+---------------------------------------
+file name   : bioconductor-rbgl-1.56.0-r341hfc679d8_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.56.0
+build       : r341hfc679d8_0
+build number: 0
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.56.0-r341hfc679d8_0.tar.bz2
+md5         : aea1101898fa498126960aea3840343d
+timestamp   : 2018-10-13 00:28:06 UTC
+dependencies: 
+  - bioconductor-graph >=1.58.0,<1.60.0
+  - libgcc-ng >=4.9
+  - libstdcxx-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-rbgl 1.56.0 r351hfc679d8_0
+---------------------------------------
+file name   : bioconductor-rbgl-1.56.0-r351hfc679d8_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.56.0
+build       : r351hfc679d8_0
+build number: 0
+size        : 3.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.56.0-r351hfc679d8_0.tar.bz2
+md5         : 0472987820398a0709728b9227c547e2
+timestamp   : 2018-10-13 00:26:11 UTC
+dependencies: 
+  - bioconductor-graph >=1.58.0,<1.60.0
+  - libgcc-ng >=4.9
+  - libstdcxx-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rbgl 1.58.1 r351hf484d3e_0
+---------------------------------------
+file name   : bioconductor-rbgl-1.58.1-r351hf484d3e_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.58.1
+build       : r351hf484d3e_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.58.1-r351hf484d3e_0.tar.bz2
+md5         : 3733b2238019443dc97da69a47d65029
+timestamp   : 2018-12-10 21:34:04 UTC
+dependencies: 
+  - bioconductor-graph >=1.60.0,<1.61.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rbgl 1.58.2 r351hf484d3e_0
+---------------------------------------
+file name   : bioconductor-rbgl-1.58.2-r351hf484d3e_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.58.2
+build       : r351hf484d3e_0
+build number: 0
+size        : 2.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.58.2-r351hf484d3e_0.tar.bz2
+md5         : 7c0cbbe585043d20fe358caee90fc517
+timestamp   : 2019-04-28 05:39:11 UTC
+dependencies: 
+  - bioconductor-graph >=1.60.0,<1.61.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rbgl 1.60.0 r36he1b5a44_1
+--------------------------------------
+file name   : bioconductor-rbgl-1.60.0-r36he1b5a44_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.60.0
+build       : r36he1b5a44_1
+build number: 1
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.60.0-r36he1b5a44_1.tar.bz2
+md5         : 105b5a14aabe4b1f3b226c0b410d5e0b
+timestamp   : 2019-07-22 05:55:57 UTC
+dependencies: 
+  - bioconductor-graph >=1.62.0,<1.63.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.62.1 r36he1b5a44_0
+--------------------------------------
+file name   : bioconductor-rbgl-1.62.1-r36he1b5a44_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.62.1
+build       : r36he1b5a44_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.62.1-r36he1b5a44_0.tar.bz2
+md5         : f32eca5084ab30ee7b1cf5f43ebe705b
+timestamp   : 2019-11-02 02:17:55 UTC
+dependencies: 
+  - bioconductor-graph >=1.64.0,<1.65.0
+  - libgcc-ng >=7.3.0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.64.0 r40h5f743cb_0
+--------------------------------------
+file name   : bioconductor-rbgl-1.64.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.64.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.64.0-r40h5f743cb_0.tar.bz2
+md5         : c5e9f5ce663d39d6df1f9a9d846fc0ba
+timestamp   : 2020-05-09 23:28:13 UTC
+dependencies: 
+  - bioconductor-graph >=1.66.0,<1.67.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - libstdcxx-ng >=7.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.66.0 r40h399db7b_1
+--------------------------------------
+file name   : bioconductor-rbgl-1.66.0-r40h399db7b_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.66.0
+build       : r40h399db7b_1
+build number: 1
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.66.0-r40h399db7b_1.tar.bz2
+md5         : d7b780572f85920a0570b9b1cd623045
+timestamp   : 2021-03-28 12:26:28 UTC
+dependencies: 
+  - bioconductor-graph >=1.68.0,<1.69.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.66.0 r40h5f743cb_0
+--------------------------------------
+file name   : bioconductor-rbgl-1.66.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.66.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.66.0-r40h5f743cb_0.tar.bz2
+md5         : 56a5319263eb549e81cf4e369a56e856
+timestamp   : 2020-10-30 11:29:45 UTC
+dependencies: 
+  - bioconductor-graph >=1.68.0,<1.69.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=7.5.0
+  - r-base >=4.0,<4.1.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.68.0 r41h399db7b_0
+--------------------------------------
+file name   : bioconductor-rbgl-1.68.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.68.0
+build       : r41h399db7b_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.68.0-r41h399db7b_0.tar.bz2
+md5         : 12b4d4c1229bd865b152ae96f52f55fb
+timestamp   : 2021-05-31 02:20:15 UTC
+dependencies: 
+  - bioconductor-graph >=1.70.0,<1.71.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.70.0 r41h399db7b_0
+--------------------------------------
+file name   : bioconductor-rbgl-1.70.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.70.0
+build       : r41h399db7b_0
+build number: 0
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.70.0-r41h399db7b_0.tar.bz2
+md5         : b9756194bb480dfe948a2e0c995d1170
+timestamp   : 2021-11-02 21:42:16 UTC
+dependencies: 
+  - bioconductor-graph >=1.72.0,<1.73.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.4.0
+  - r-base >=4.1,<4.2.0a0
+  - r-bh
+
+
+bioconductor-rbgl 1.70.0 r41h619a076_1
+--------------------------------------
+file name   : bioconductor-rbgl-1.70.0-r41h619a076_1.tar.bz2
+name        : bioconductor-rbgl
+version     : 1.70.0
+build       : r41h619a076_1
+build number: 1
+size        : 2.7 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rbgl-1.70.0-r41h619a076_1.tar.bz2
+md5         : f5eadeed415e1e0b3d22ccd5f

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-regionalst.manual_bundle.txt

@@ -0,0 +1,92 @@
+# Tool: bioconductor-regionalst
+software_name: bioconductor-regionalst
+tier: T1
+domain: single_cell
+downloads: 1301
+summary: Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data
+description: This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.
+dependencies: bioconductor-bayesspace >=1.20.0,<1.21.0, bioconductor-biocstyle >=2.38.0,<2.39.0, bioconductor-fgsea >=1.36.0,<1.37.0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-scater >=1.38.0,<1.39.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, bioconductor-toast >=1.24.0,<1.25.0, r-assertthat, r-base >=4.5,<4.6.0a0, r-colorspace, r-dplyr, r-ggplot2, r-gridextra, r-magrittr, r-rcolorbrewer, r-seurat, r-shiny, r-tibble
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.18/bioc/html/RegionalST.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.18/bioc/html/RegionalST.html
+Bioconductor - RegionalST About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.18 Software Packages RegionalST RegionalST This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see RegionalST . Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data DOI: 10.18129/B9.bioc.RegionalST Bioconductor version: 3.18 This package analyze spatial transcriptomics data through cross-regional analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application. Author: Ziyi Li [aut, cre] Maintainer: Ziyi Li &#x3c;&#x7a;&#x6c;&#x69;&#x31;&#x36;&#x20;&#x61;&#x74;&#x20;&#x6d;&#x64;&#x61;&#x6e;&#x64;&#x65;&#x72;&#x73;&#x6f;&#x6e;&#x2e;&#x6f;&#x72;&#x67;&#x3e; Citation (from within R, enter citation("RegionalST") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("RegionalST") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("RegionalST") RegionalST HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews KEGG , Reactome , Software , Spatial , Transcriptomics Version 1.0.1 In Bioconductor since BioC 3.18 (R-4.3) (0.5 years) License GPL-3 Depends R (>= 4.3.0) Imports stats, grDevices, utils, ggplot2, dplyr, scater , gridExtra, BayesSpace , fgsea , magrittr, SingleCellExperiment , RColorBrewer, Seurat, S4Vectors , tibble, TOAST , assertthat, colorspace, shiny, SummarizedExperiment System Requirements URL See More Suggests BiocStyle , knitr, rmarkdown, gplots, testthat (>= 3.0.0) Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package RegionalST_1.0.1.tar.gz Windows Binary RegionalST_1.0.1.zip (64-bit only) macOS Binary (x86_64) RegionalST_1.0.1.tgz macOS Binary (arm64) RegionalST_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/RegionalST Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RegionalST Bioc Package Browser https://code.bioconductor.org/browse/RegionalST/ Package Short Url https://bioconductor.org/packages/RegionalST/ Package Downloads Report Download Stats Old Source Packages for BioC 3.18 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-regionalst --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-regionalst 1.0.1 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-regionalst-1.0.1-r43hdfd78af_0.tar.bz2
+name        : bioconductor-regionalst
+version     : 1.0.1
+build       : r43hdfd78af_0
+build number: 0
+size        : 2.9 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-regionalst-1.0.1-r43hdfd78af_0.tar.bz2
+md5         : 58a377f7d6c56cdfc8a9eafc6643a388
+timestamp   : 2023-12-12 00:34:18 UTC
+dependencies: 
+  - bioconductor-bayesspace >=1.12.0,<1.13.0
+  - bioconductor-fgsea >=1.28.0,<1.29.0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-scater >=1.30.0,<1.31.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - bioconductor-toast >=1.16.0,<1.17.0
+  - r-assertthat
+  - r-base >=4.3,<4.4.0a0
+  - r-colorspace
+  - r-dplyr
+  - r-ggplot2
+  - r-gridextra
+  - r-magrittr
+  - r-rcolorbrewer
+  - r-seurat
+  - r-shiny
+  - r-tibble
+
+
+bioconductor-regionalst 1.8.0 r45hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-regionalst-1.8.0-r45hdfd78af_0.conda
+name        : bioconductor-regionalst
+version     : 1.8.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 3.7 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-regionalst-1.8.0-r45hdfd78af_0.conda
+md5         : f2ecbde0b5cd6df9b7bc3a1a7baa5356
+timestamp   : 2026-03-03 21:04:11 UTC
+dependencies: 
+  - bioconductor-bayesspace >=1.20.0,<1.21.0
+  - bioconductor-biocstyle >=2.38.0,<2.39.0
+  - bioconductor-fgsea >=1.36.0,<1.37.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-scater >=1.38.0,<1.39.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - bioconductor-toast >=1.24.0,<1.25.0
+  - r-assertthat
+  - r-base >=4.5,<4.6.0a0
+  - r-colorspace
+  - r-dplyr
+  - r-ggplot2
+  - r-gridextra
+  - r-magrittr
+  - r-rcolorbrewer
+  - r-seurat
+  - r-shiny
+  - r-tibble

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rgraphviz.manual_bundle.txt

@@ -0,0 +1,422 @@
+# Tool: bioconductor-rgraphviz
+software_name: bioconductor-rgraphviz
+tier: T1
+domain: t1_backfill_overall
+downloads: 129127
+summary: Provides plotting capabilities for R graph objects
+description: Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.
+dependencies: bioconductor-graph >=1.88.0,<1.89.0, bioconductor-graph >=1.88.1,<1.89.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.3,<6.0a0, libstdcxx >=14, libzlib >=1.3.2,<2.0a0, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/Rgraphviz.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/Rgraphviz.html
+Bioconductor - Rgraphviz Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Rgraphviz Rgraphviz This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Rgraphviz . Provides plotting capabilities for R graph objects DOI: 10.18129/B9.bioc.Rgraphviz Bioconductor version: 3.22 Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Author: Kasper Daniel Hansen [cre, aut], Jeff Gentry [aut], Li Long [aut], Robert Gentleman [aut], Seth Falcon [aut], Florian Hahne [aut], Deepayan Sarkar [aut] Maintainer: Kasper Daniel Hansen &#x3c;&#x6b;&#x61;&#x73;&#x70;&#x65;&#x72;&#x64;&#x61;&#x6e;&#x69;&#x65;&#x6c;&#x68;&#x61;&#x6e;&#x73;&#x65;&#x6e;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("Rgraphviz") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rgraphviz") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Rgraphviz") A New Interface to Plot Graphs Using Rgraphviz PDF R Script How To Plot A Graph Using Rgraphviz PDF R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews GraphAndNetwork , Software , Visualization Version 2.54.0 In Bioconductor since BioC 1.6 (R-2.1) or earlier (&gt; 21 years) License EPL Depends R (>= 2.6.0), methods, utils, graph , grid Imports stats4, graphics, grDevices System Requirements optionally Graphviz (>= 2.16), USE_C17 URL See More Suggests RUnit , BiocGenerics , XML Linking To Enhances Depends On Me biocGraph , BioMVCClass , CellNOptR , MineICA , netresponse , paircompviz , pathRender , ROntoTools , SplicingGraphs , maEndToEnd , dlsem , gridGraphviz Imports Me apComplex , biocGraph , bnem , chimeraviz , CytoML , DEGraph , EnrichDO , EnrichmentBrowser , flowWorkspace , GeneNetworkBuilder , GOstats , hyperdraw , KEGGgraph , mirIntegrator , MIRit , mnem , OncoSimulR , ontoProc , paircompviz , pathview , Pigengene , qpgraph , TRONCO , abn , agena.ai , BCDAG , BiDAG , bnpa , bnRep , CePa , classGraph , cogmapr , ontologyPlot , SEMgraph , stablespec , WayFindR Suggests Me a4 , altcdfenvs , annotate , Category , CNORfeeder , CNORfuzzy , DEGraph , flowCore , geneplotter , GlobalAncova , globaltest , GSEABase , MLP , NCIgraph , RBGL , rBiopaxParser , safe , SPIA , SRAdb , Streamer , topGO , ViSEAGO , vtpnet , NCIgraphData , SNAData , arulesViz , BayesNetBP , bivarhr , bnlearn , bnstruct , ChoR , CodeDepends , gbutils , GeneNet , gRain , iTOP , kst , lava , loon , maGUI , micd , multiplex , netmeta , pcalg , PCBN , pchc , pks , psych , rCausalMGM , relations , rEMM , rPref , rSpectral , SCCI , sisal , textplot , tm , topologyGSA , tpc , unifDAG , zenplots Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rgraphviz_2.54.0.tar.gz Windows Binary (x86_64) Rgraphviz_2.54.0.zip macOS Binary (x86_64) Rgraphviz_2.54.0.tgz macOS Binary (arm64) Rgraphviz_2.54.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rgraphviz Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rgraphviz Bioc Package Browser https://code.bioconductor.org/browse/Rgraphviz/ Package Short Url https://bioconductor.org/packages/Rgraphviz/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-rgraphviz --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-rgraphviz 2.13.0 0
+-------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : 0
+build number: 0
+size        : 860 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-0.tar.bz2
+md5         : 722ad7942f3c2bca5845a608d319d855
+dependencies: 
+  - bioconductor-graph
+  - r >=2.6.0
+
+
+bioconductor-rgraphviz 2.13.0 r3.3.1_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-r3.3.1_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : r3.3.1_0
+build number: 0
+size        : 866 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.3.1_0.tar.bz2
+md5         : 59d71039ccb54b254bddbae64ef998a7
+dependencies: 
+  - bioconductor-graph
+  - r 3.3.1*
+
+
+bioconductor-rgraphviz 2.13.0 r3.3.2_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-r3.3.2_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : r3.3.2_0
+build number: 0
+size        : 866 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.3.2_0.tar.bz2
+md5         : 13457e492fb002c62d389a47ecf6d1b8
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.3.2*
+
+
+bioconductor-rgraphviz 2.13.0 r3.4.1_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : r3.4.1_0
+build number: 0
+size        : 880 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r3.4.1_0.tar.bz2
+md5         : 2324b2ab5d6530dfb74e35c733915f5d
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.4.1*
+
+
+bioconductor-rgraphviz 2.13.0 r341_1
+------------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-r341_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : r341_1
+build number: 1
+size        : 884 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r341_1.tar.bz2
+md5         : 519ee006e04a1b432ff6bbe405f16ad2
+timestamp   : 2018-10-13 01:09:32 UTC
+dependencies: 
+  - bioconductor-graph
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-rgraphviz 2.13.0 r351_1
+------------------------------------
+file name   : bioconductor-rgraphviz-2.13.0-r351_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.13.0
+build       : r351_1
+build number: 1
+size        : 991 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.13.0-r351_1.tar.bz2
+md5         : 58b41ddc8c01c724bb13e501c9bd1a98
+timestamp   : 2018-10-13 01:07:41 UTC
+dependencies: 
+  - bioconductor-graph
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rgraphviz 2.14.0 0
+-------------------------------
+file name   : bioconductor-rgraphviz-2.14.0-0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.14.0
+build       : 0
+build number: 0
+size        : 1.4 MB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.14.0-0.tar.bz2
+md5         : 3066ac60dca8caa320798ebe069434c6
+dependencies: 
+  - bioconductor-graph
+  - r >=2.6.0
+
+
+bioconductor-rgraphviz 2.16.0 r3.3.1_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.16.0-r3.3.1_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.16.0
+build       : r3.3.1_0
+build number: 0
+size        : 862 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.1_0.tar.bz2
+md5         : 77e2930aee50b5cd13e609678251a7ba
+dependencies: 
+  - bioconductor-graph
+  - r 3.3.1*
+
+
+bioconductor-rgraphviz 2.16.0 r3.3.1_1
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.16.0-r3.3.1_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.16.0
+build       : r3.3.1_1
+build number: 1
+size        : 861 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.1_1.tar.bz2
+md5         : f6af84f695bbcc53309dae51f4f5e560
+dependencies: 
+  - bioconductor-graph
+  - libgcc
+  - r 3.3.1*
+
+
+bioconductor-rgraphviz 2.16.0 r3.3.2_1
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.16.0-r3.3.2_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.16.0
+build       : r3.3.2_1
+build number: 1
+size        : 863 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.3.2_1.tar.bz2
+md5         : cf1a24559b2c4d96d690614927a33c31
+dependencies: 
+  - bioconductor-graph
+  - libgcc
+  - r-base 3.3.2*
+
+
+bioconductor-rgraphviz 2.16.0 r3.4.1_1
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.16.0-r3.4.1_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.16.0
+build       : r3.4.1_1
+build number: 1
+size        : 876 KB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.16.0-r3.4.1_1.tar.bz2
+md5         : 1a70d20f58311b6e955aeff3895be111
+dependencies: 
+  - bioconductor-graph
+  - libgcc
+  - r-base 3.4.1*
+
+
+bioconductor-rgraphviz 2.20.0 r3.4.1_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.20.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.20.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.4 MB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.20.0-r3.4.1_0.tar.bz2
+md5         : 894e6bf65d0a4190492253bf028172c7
+dependencies: 
+  - bioconductor-graph
+  - r-base 3.4.1*
+
+
+bioconductor-rgraphviz 2.20.0 r3.4.1_1
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.20.0-r3.4.1_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.20.0
+build       : r3.4.1_1
+build number: 1
+size        : 1.4 MB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.20.0-r3.4.1_1.tar.bz2
+md5         : d5f5db50b05d5d6d11760185550e7fb5
+dependencies: 
+  - bioconductor-graph
+  - libgcc
+  - r-base 3.4.1*
+
+
+bioconductor-rgraphviz 2.22.0 r3.4.1_0
+--------------------------------------
+file name   : bioconductor-rgraphviz-2.22.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.22.0
+build       : r3.4.1_0
+build number: 0
+size        : 1.4 MB
+license     : EPL
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.22.0-r3.4.1_0.tar.bz2
+md5         : d9afb234e02f26ff35121033de8def5e
+dependencies: 
+  - bioconductor-graph
+  - libgcc
+  - r-base 3.4.1*
+
+
+bioconductor-rgraphviz 2.24.0 r341hfc679d8_0
+--------------------------------------------
+file name   : bioconductor-rgraphviz-2.24.0-r341hfc679d8_0.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.24.0
+build       : r341hfc679d8_0
+build number: 0
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+  - r-base >=3.4.1,<3.4.2.0a0
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+bioconductor-rgraphviz 2.24.0 r351hfc679d8_0
+--------------------------------------------
+file name   : bioconductor-rgraphviz-2.24.0-r351hfc679d8_0.tar.bz2
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+  - r-base >=3.5.1,<3.5.2.0a0
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+--------------------------------------------
+file name   : bioconductor-rgraphviz-2.26.0-r351hf484d3e_0.tar.bz2
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+md5         : efe22a97679cb1250f62f812d5bf5feb
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+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rgraphviz 2.28.0 r36he1b5a44_1
+-------------------------------------------
+file name   : bioconductor-rgraphviz-2.28.0-r36he1b5a44_1.tar.bz2
+name        : bioconductor-rgraphviz
+version     : 2.28.0
+build       : r36he1b5a44_1
+build number: 1
+size        : 1.5 MB
+license     : EPL
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.28.0-r36he1b5a44_1.tar.bz2
+md5         : 9f454621d8c5e837364041fc2cdc2b08
+timestamp   : 2019-07-22 09:33:59 UTC
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+
+bioconductor-rgraphviz 2.30.0 r36he1b5a44_0
+-------------------------------------------
+file name   : bioconductor-rgraphviz-2.30.0-r36he1b5a44_0.tar.bz2
+name        : bioconductor-rgraphviz
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+md5         : 9d8a5d1b32362652996391f825d09d85
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+  - libstdcxx-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
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+
+bioconductor-rgraphviz 2.32.0 r40h5f743cb_0
+-------------------------------------------
+file name   : bioconductor-rgraphviz-2.32.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-rgraphviz
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+license     : EPL
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+md5         : f3110fe03353189dd3fd81e146a8a6c5
+timestamp   : 2020-05-10 06:28:31 UTC
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+  - r-base >=4.0,<4.1.0a0
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+
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+-------------------------------------------
+file name   : bioconductor-rgraphviz-2.34.0-r40h399db7b_1.tar.bz2
+name        : bioconductor-rgraphviz
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+license     : EPL
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rgraphviz-2.34.0-r40h399db7b_1.tar.bz2
+md5         : 289be0c26a744f38ac2ce6656c14adda
+timestamp   : 2021-03-29 11:24:48 UTC
+dependencies: 
+  - bioconductor-graph >=1.68.0,<1.69.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5filters.manual_bundle.txt

@@ -0,0 +1,366 @@
+# Tool: bioconductor-rhdf5filters
+software_name: bioconductor-rhdf5filters
+tier: T1
+domain: t1_backfill_overall
+downloads: 565355
+summary: HDF5 Compression Filters
+description: Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.
+dependencies: bioconductor-rhdf5lib >=1.32.0,<1.33.0, bioconductor-rhdf5lib >=1.32.0,<1.33.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libstdcxx >=14, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.11/bioc/html/rhdf5filters.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.11/bioc/html/rhdf5filters.html
+Bioconductor - rhdf5filters About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.11 Software Packages rhdf5filters rhdf5filters This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see rhdf5filters . HDF5 Compression Filters DOI: 10.18129/B9.bioc.rhdf5filters Bioconductor version: 3.11 Provides a collection of compression filters for use with HDF5 datasets. Author: Mike Smith [aut, cre] Maintainer: Mike Smith &#x3c;&#x67;&#x72;&#x69;&#x6d;&#x62;&#x6f;&#x75;&#x67;&#x68;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("rhdf5filters") ): Installation To install this package, start R (version "4.0") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("rhdf5filters") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("rhdf5filters") HDF5 Compression Filters HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataImport , Infrastructure , Software Version 1.0.1 In Bioconductor since BioC 3.11 (R-4.0) (4 years) License BSD_2_clause + file LICENSE Depends Imports System Requirements GNU make URL https://github.com/grimbough/rhdf5filters Bug Reports https://github.com/grimbough/rhdf5filters See More Suggests BiocStyle , knitr, rmarkdown, testthat (>= 2.1.0) Linking To Rhdf5lib Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package rhdf5filters_1.0.1.tar.gz Windows Binary rhdf5filters_1.0.1.zip (32- &amp; 64-bit) macOS 10.13 (High Sierra) rhdf5filters_1.0.1.tgz Source Repository git clone https://git.bioconductor.org/packages/rhdf5filters Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rhdf5filters Bioc Package Browser https://code.bioconductor.org/browse/rhdf5filters/ Package Short Url https://bioconductor.org/packages/rhdf5filters/ Package Downloads Report Download Stats Old Source Packages for BioC 3.11 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-rhdf5filters --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-rhdf5filters 1.2.0 r40h399db7b_1
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.2.0-r40h399db7b_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.2.0
+build       : r40h399db7b_1
+build number: 1
+size        : 639 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.2.0-r40h399db7b_1.tar.bz2
+md5         : 0846bf2cedfcad320ff650957132839e
+timestamp   : 2021-03-25 03:49:07 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.12.0,<1.13.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-rhdf5filters 1.2.0 r40h5f743cb_0
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.2.0-r40h5f743cb_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.2.0
+build       : r40h5f743cb_0
+build number: 0
+size        : 629 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.2.0-r40h5f743cb_0.tar.bz2
+md5         : c7dca2e73dbe4a2ed2c3335bb9f741bf
+timestamp   : 2020-10-29 17:05:55 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.12.0,<1.13.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=7.5.0
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-rhdf5filters 1.4.0 r41h399db7b_0
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.4.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.4.0
+build       : r41h399db7b_0
+build number: 0
+size        : 661 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.4.0-r41h399db7b_0.tar.bz2
+md5         : f7f85b739e9fab6deaa5847597951c9d
+timestamp   : 2021-05-31 06:32:11 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.14.0,<1.15.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.3.0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5filters 1.6.0 r41h399db7b_0
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.6.0-r41h399db7b_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.6.0
+build       : r41h399db7b_0
+build number: 0
+size        : 664 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41h399db7b_0.tar.bz2
+md5         : 204b7a8e97b5819c7132cbf4a93db414
+timestamp   : 2021-11-02 02:31:33 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.16.0,<1.17.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=9.4.0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5filters 1.6.0 r41h619a076_1
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.6.0-r41h619a076_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.6.0
+build       : r41h619a076_1
+build number: 1
+size        : 655 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41h619a076_1.tar.bz2
+md5         : d2e66a1e4b30c31abe9e3ac262a23f82
+timestamp   : 2022-02-23 21:56:14 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.16.0,<1.17.0
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - libstdcxx-ng >=10.3.0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5filters 1.6.0 r41hc247a5b_2
+---------------------------------------------
+file name   : bioconductor-rhdf5filters-1.6.0-r41hc247a5b_2.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.6.0
+build       : r41hc247a5b_2
+build number: 2
+size        : 646 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.6.0-r41hc247a5b_2.tar.bz2
+md5         : 3658bb6ad33ee34cc7b315d1ff3a4ef2
+timestamp   : 2022-09-15 10:20:40 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.16.0,<1.17.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5filters 1.10.0 r42hc247a5b_0
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.10.0-r42hc247a5b_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.10.0
+build       : r42hc247a5b_0
+build number: 0
+size        : 758 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.10.0-r42hc247a5b_0.tar.bz2
+md5         : 1c3ee5bc6c32455512844afe359f6baa
+timestamp   : 2022-11-03 14:27:23 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.20.0,<1.21.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-rhdf5filters 1.10.0 r42hf17093f_1
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.10.0-r42hf17093f_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.10.0
+build       : r42hf17093f_1
+build number: 1
+size        : 763 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.10.0-r42hf17093f_1.tar.bz2
+md5         : a68b0be19881807360a989f01f9b9f75
+timestamp   : 2023-05-18 16:32:14 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.20.0,<1.21.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-rhdf5filters 1.12.1 r43hf17093f_0
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.12.1-r43hf17093f_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.12.1
+build       : r43hf17093f_0
+build number: 0
+size        : 1.0 MB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.12.1-r43hf17093f_0.tar.bz2
+md5         : 60491d28b8627339fbeb567cba682765
+timestamp   : 2023-07-07 12:26:15 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.22.0,<1.23.0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-rhdf5filters 1.12.1 r43hf17093f_1
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.12.1-r43hf17093f_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.12.1
+build       : r43hf17093f_1
+build number: 1
+size        : 1.1 MB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.12.1-r43hf17093f_1.tar.bz2
+md5         : 783b9fe64acb8aaf325fa2e913bef3cb
+timestamp   : 2023-10-27 18:14:10 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.22.0,<1.23.0
+  - bioconductor-rhdf5lib >=1.22.0,<1.23.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-rhdf5filters 1.14.1 r43hf17093f_0
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.14.1-r43hf17093f_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.14.1
+build       : r43hf17093f_0
+build number: 0
+size        : 555 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.14.1-r43hf17093f_0.tar.bz2
+md5         : eff861de3afd924ac05a2726f8b284f9
+timestamp   : 2023-12-04 03:01:07 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.24.0,<1.25.0
+  - bioconductor-rhdf5lib >=1.24.0,<1.25.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-rhdf5filters 1.14.1 r43hf17093f_1
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.14.1-r43hf17093f_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.14.1
+build       : r43hf17093f_1
+build number: 1
+size        : 559 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.14.1-r43hf17093f_1.tar.bz2
+md5         : 9ee7c8344b04f246477e9aa58ee52f11
+timestamp   : 2024-05-07 18:59:59 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.24.0,<1.25.0
+  - bioconductor-rhdf5lib >=1.24.0,<1.25.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx-ng >=12
+  - r-base >=4.3,<4.4.0a0
+
+
+bioconductor-rhdf5filters 1.18.0 r44h77050f0_0
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.18.0-r44h77050f0_0.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.18.0
+build       : r44h77050f0_0
+build number: 0
+size        : 564 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.18.0-r44h77050f0_0.tar.bz2
+md5         : d1f365d0504d628a27c3d0749224da10
+timestamp   : 2024-12-18 15:11:40 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.28.0,<1.29.0
+  - bioconductor-rhdf5lib >=1.28.0,<1.29.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  - r-base >=4.4,<4.5.0a0
+
+
+bioconductor-rhdf5filters 1.18.0 r44h77050f0_1
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.18.0-r44h77050f0_1.tar.bz2
+name        : bioconductor-rhdf5filters
+version     : 1.18.0
+build       : r44h77050f0_1
+build number: 1
+size        : 554 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.18.0-r44h77050f0_1.tar.bz2
+md5         : 290eb5bda03045128590f20568593b52
+timestamp   : 2025-04-21 08:31:25 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.28.0,<1.29.0
+  - bioconductor-rhdf5lib >=1.28.0,<1.29.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - libstdcxx >=13
+  - libzlib >=1.3.1,<2.0a0
+  - r-base >=4.4,<4.5.0a0
+
+
+bioconductor-rhdf5filters 1.22.0 r45ha27e39d_0
+----------------------------------------------
+file name   : bioconductor-rhdf5filters-1.22.0-r45ha27e39d_0.conda
+name        : bioconductor-rhdf5filters
+version     : 1.22.0
+build       : r45ha27e39d_0
+build number: 0
+size        : 500 KB
+license     : BSD_2_clause + file LICENSE
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5filters-1.22.0-r45ha27e39d_0.conda
+md5         : bb1531739e103b2433b5e75e23bed547
+timestamp   : 2026-02-07 23:48:25 UTC
+dependencies: 
+  - bioconductor-rhdf5lib >=1.32.0,<1.33.0
+  - bioconductor-rhdf5lib >=1.32.0,<1.33.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=14
+  - liblapack >=3.9.0,<4.0a0
+  - liblzma >=5.8.2,<6.0a0
+  - libstdcxx >=14
+  - libzlib >=1.3.1,<2.0a0
+  - r-base >=4.5,<4.6.0a0

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rhdf5lib.manual_bundle.txt

@@ -0,0 +1,387 @@
+# Tool: bioconductor-rhdf5lib
+software_name: bioconductor-rhdf5lib
+tier: T1
+domain: t1_backfill_overall
+downloads: 667943
+summary: hdf5 library as an R package
+description: Provides C and C++ hdf5 libraries.
+dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: http://bioconductor.org/packages/3.6/bioc/html/Rhdf5lib.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### http://bioconductor.org/packages/3.6/bioc/html/Rhdf5lib.html
+Bioconductor - Rhdf5lib About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.6 Software Packages Rhdf5lib Rhdf5lib This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see Rhdf5lib . hdf5 library as an R package DOI: 10.18129/B9.bioc.Rhdf5lib Bioconductor version: 3.6 Provides C and C++ hdf5 libraries. Author: Mike Smith Maintainer: Mike Smith &#x3c;&#x67;&#x72;&#x69;&#x6d;&#x62;&#x6f;&#x75;&#x67;&#x68;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("Rhdf5lib") ): Installation To install this package, start R (version "3.4") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rhdf5lib") For older versions of R, please refer to the appropriate Bioconductor release . Documentation Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Infrastructure , Software Version 1.0.0 In Bioconductor since BioC 3.6 (R-3.4) (6.5 years) License Artistic-2.0 Depends Imports System Requirements GNU make URL Bug Reports https://github.com/grimbough/Rhdf5lib See More Suggests BiocStyle , knitr, rmarkdown Linking To Enhances Depends On Me Imports Me beachmat Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rhdf5lib_1.0.0.tar.gz Windows Binary Rhdf5lib_1.0.0.zip (32- &amp; 64-bit) Mac OS X 10.11 (El Capitan) Rhdf5lib_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rhdf5lib Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rhdf5lib Package Short Url https://bioconductor.org/packages/Rhdf5lib/ Package Downloads Report Download Stats Old Source Packages for BioC 3.6 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-rhdf5lib --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-rhdf5lib 1.0.0 r3.4.1_0
+------------------------------------
+file name   : bioconductor-rhdf5lib-1.0.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.0.0
+build       : r3.4.1_0
+build number: 0
+size        : 2.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.0.0-r3.4.1_0.tar.bz2
+md5         : 81ae070aac81cc3a62dbfc0856222d13
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-rhdf5lib 1.2.1 r341h470a237_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.2.1-r341h470a237_0.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.2.1
+build       : r341h470a237_0
+build number: 0
+size        : 2.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.2.1-r341h470a237_0.tar.bz2
+md5         : 053446586a3f3c33b177eb1d49ffd56d
+timestamp   : 2018-10-10 09:23:01 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-rhdf5lib 1.2.1 r351h470a237_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.2.1-r351h470a237_0.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.2.1
+build       : r351h470a237_0
+build number: 0
+size        : 2.8 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.2.1-r351h470a237_0.tar.bz2
+md5         : d24a22b6c11a2b96bf4a480209242d22
+timestamp   : 2018-10-10 09:20:14 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rhdf5lib 1.4.2 r351h1feb10b_3
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.4.2-r351h1feb10b_3.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.4.2
+build       : r351h1feb10b_3
+build number: 3
+size        : 3.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.2-r351h1feb10b_3.tar.bz2
+md5         : 2d341286ccabbb70cfa6e90a5e2d3f4e
+timestamp   : 2019-02-13 10:39:04 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - zlib >=1.2.11,<1.3.0a0
+
+
+bioconductor-rhdf5lib 1.4.2 r351h9c0d707_2
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.4.2-r351h9c0d707_2.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.4.2
+build       : r351h9c0d707_2
+build number: 2
+size        : 3.5 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.2-r351h9c0d707_2.tar.bz2
+md5         : 5986a988aa7a85abebc11515de168609
+timestamp   : 2019-01-26 20:00:26 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - libgfortran >=3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - zlib >=1.2.11,<1.3.0a0
+
+
+bioconductor-rhdf5lib 1.4.3 r351h1feb10b_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.4.3-r351h1feb10b_0.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.4.3
+build       : r351h1feb10b_0
+build number: 0
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.4.3-r351h1feb10b_0.tar.bz2
+md5         : d08f19c5a143241c4075c83ee55372b6
+timestamp   : 2019-03-24 09:24:26 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - libgfortran-ng >=7,<8.0a0
+  - r-base >=3.5.1,<3.5.2.0a0
+  - zlib >=1.2.11,<1.3.0a0
+
+
+bioconductor-rhdf5lib 1.6.0 r351h14c3975_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.6.0-r351h14c3975_0.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.6.0
+build       : r351h14c3975_0
+build number: 0
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.6.0-r351h14c3975_0.tar.bz2
+md5         : 8ab901fb884944ee155d2cace06129c8
+timestamp   : 2019-05-08 11:45:19 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rhdf5lib 1.6.0 r36h516909a_1
+-----------------------------------------
+file name   : bioconductor-rhdf5lib-1.6.0-r36h516909a_1.tar.bz2
+name        : bioconductor-rhdf5lib
+version     : 1.6.0
+build       : r36h516909a_1
+build number: 1
+size        : 3.6 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.6.0-r36h516909a_1.tar.bz2
+md5         : 1023caa12443a0730d31af3a0ddb5ce5
+timestamp   : 2019-07-21 13:25:50 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-rhdf5lib 1.8.0 r36h516909a_0
+-----------------------------------------
+file name   : bioconductor-rhdf5lib-1.8.0-r36h516909a_0.tar.bz2
+name        : bioconductor-rhdf5lib
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+license     : Artistic-2.0
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+md5         : 408ceb14368c386c723df14b5ec9e6ee
+timestamp   : 2019-11-01 14:47:58 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-rhdf5lib 1.10.0 r40h037d062_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.10.0-r40h037d062_0.tar.bz2
+name        : bioconductor-rhdf5lib
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+md5         : 1daca590fc3da936b02427270da41469
+timestamp   : 2020-05-09 09:30:01 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-rhdf5lib 1.12.0 r40h037d062_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.12.0-r40h037d062_0.tar.bz2
+name        : bioconductor-rhdf5lib
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+license     : Artistic-2.0
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+md5         : 70f8b21e7077b2e980a9105630697d6a
+timestamp   : 2020-10-29 16:52:10 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.0,<4.1.0a0
+
+
+bioconductor-rhdf5lib 1.12.1 r40hd029910_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.12.1-r40hd029910_0.tar.bz2
+name        : bioconductor-rhdf5lib
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+md5         : c92e8f8616558edd120894c5b3f2c320
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+
+bioconductor-rhdf5lib 1.14.0 r41hd029910_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.14.0-r41hd029910_0.tar.bz2
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+md5         : 825074e2fa0d6c518790f842fd18cda8
+timestamp   : 2021-05-31 01:17:11 UTC
+dependencies: 
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+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5lib 1.16.0 r41h5c21468_1
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.16.0-r41h5c21468_1.tar.bz2
+name        : bioconductor-rhdf5lib
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41h5c21468_1.tar.bz2
+md5         : 18d81acd3db5186d3ad575dae7812d3a
+timestamp   : 2022-02-21 20:50:10 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5lib 1.16.0 r41hc0cfd56_2
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.16.0-r41hc0cfd56_2.tar.bz2
+name        : bioconductor-rhdf5lib
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+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41hc0cfd56_2.tar.bz2
+md5         : 65a831c2e26f30f76eb8cd27498a1320
+timestamp   : 2022-09-15 09:59:32 UTC
+dependencies: 
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5lib 1.16.0 r41hd029910_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.16.0-r41hd029910_0.tar.bz2
+name        : bioconductor-rhdf5lib
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+size        : 3.9 MB
+license     : Artistic-2.0
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+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.16.0-r41hd029910_0.tar.bz2
+md5         : c0bdbd74f8eca322bf453c229c5d5869
+timestamp   : 2021-11-01 15:30:55 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+
+
+bioconductor-rhdf5lib 1.20.0 r42ha9d7317_2
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.20.0-r42ha9d7317_2.tar.bz2
+name        : bioconductor-rhdf5lib
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+build number: 2
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+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.20.0-r42ha9d7317_2.tar.bz2
+md5         : b8050b2dc519548201872884ae4ee186
+timestamp   : 2023-05-16 14:23:44 UTC
+dependencies: 
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-rhdf5lib 1.20.0 r42hc0cfd56_0
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_0.tar.bz2
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+md5         : e2fe9002e7345aaa7aef9dcb601cdede
+timestamp   : 2022-11-03 14:16:34 UTC
+dependencies: 
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-base >=4.2,<4.3.0a0
+
+
+bioconductor-rhdf5lib 1.20.0 r42hc0cfd56_1
+------------------------------------------
+file name   : bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_1.tar.bz2
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+size        : 3.9 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhdf5lib-1.20.0-r42hc0cfd56_1.tar.bz2
+md5         : 747142d93afa8add37a47a597eebeedd
+t

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-rsubread.manual_bundle.txt

@@ -0,0 +1,413 @@
+# Tool: bioconductor-rsubread
+software_name: bioconductor-rsubread
+tier: T1
+domain: t1_backfill_overall
+downloads: 136583
+summary: Mapping, quantification and variant analysis of sequencing data
+description: Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.
+dependencies: libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-base >=4.5,<4.6.0a0, r-matrix
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.22/bioc/html/Rsubread.html
+doc_url: 
+dev_url: 
+
+## CLI Help Source
+rscript:--help
+## CLI Help Content
+$ conda run -n bioenv_r_bioc Rscript --help
+[rc=127]
+
+Rscript: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory
+
+ERROR conda.cli.main_run:execute(127): `conda run Rscript --help` failed. (See above for error)
+
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.22/bioc/html/Rsubread.html
+Bioconductor - Rsubread Bioconductor 3.23 Release! About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.22 Software Packages Rsubread Rsubread This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see Rsubread . Mapping, quantification and variant analysis of sequencing data DOI: 10.18129/B9.bioc.Rsubread Bioconductor version: 3.22 Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads. Author: Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai Maintainer: Wei Shi &#x3c;&#x77;&#x65;&#x69;&#x2e;&#x73;&#x68;&#x69;&#x32;&#x20;&#x61;&#x74;&#x20;&#x6d;&#x6f;&#x6e;&#x61;&#x73;&#x68;&#x2e;&#x65;&#x64;&#x75;&#x3e;, Yang Liao &#x3c;&#x79;&#x61;&#x6e;&#x67;&#x2e;&#x6c;&#x69;&#x61;&#x6f;&#x20;&#x61;&#x74;&#x20;&#x6d;&#x6f;&#x6e;&#x61;&#x73;&#x68;&#x2e;&#x65;&#x64;&#x75;&#x3e; and Gordon K Smyth &#x3c;&#x73;&#x6d;&#x79;&#x74;&#x68;&#x20;&#x61;&#x74;&#x20;&#x77;&#x65;&#x68;&#x69;&#x2e;&#x65;&#x64;&#x75;&#x2e;&#x61;&#x75;&#x3e; Citation (from within R, enter citation("Rsubread") ): Installation To install this package, start R (version "4.5") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Rsubread") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("Rsubread") Rsubread Vignette PDF R Script SubreadUsersGuide.pdf PDF Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews Alignment , ChIPSeq , GeneExpression , GeneFusionDetection , GeneRegulation , GeneticVariability , Genetics , GenomeAnnotation , ImmunoOncology , IndelDetection , MultipleSequenceAlignment , Preprocessing , QualityControl , RNASeq , SNP , SequenceMatching , Sequencing , SingleCell , Software , VariantAnnotation , VariantDetection Version 2.24.0 In Bioconductor since BioC 2.8 (R-2.13) (15 years) License GPL (>=3) Depends Imports grDevices, stats, utils, Matrix System Requirements URL http://bioconductor.org/packages/Rsubread See More Suggests Linking To Enhances Depends On Me ExCluster Imports Me CleanUpRNAseq , Damsel , diffUTR , dupRadar , FRASER , ribosomeProfilingQC , scPipe , scruff , stPipe Suggests Me autonomics , icetea , singleCellTK , SpliceWiz , tidybulk , MetaScope , inDAGO Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package Rsubread_2.24.0.tar.gz Windows Binary (x86_64) Rsubread_2.24.0.zip macOS Binary (x86_64) Rsubread_2.24.0.tgz macOS Binary (arm64) Rsubread_2.24.0.tgz Source Repository git clone https://git.bioconductor.org/packages/Rsubread Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rsubread Bioc Package Browser https://code.bioconductor.org/browse/Rsubread/ Package Short Url https://bioconductor.org/packages/Rsubread/ Package Downloads Report Download Stats About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2026 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-rsubread --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-rsubread 1.22.1 r3.2.2_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.22.1-r3.2.2_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.22.1
+build       : r3.2.2_0
+build number: 0
+size        : 9.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.22.1-r3.2.2_0.tar.bz2
+md5         : 9d5c24af2182f395aa495fa4d9c73ced
+dependencies: 
+  - r 3.2.2*
+
+
+bioconductor-rsubread 1.23.0 r3.3.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.23.0-r3.3.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.23.0
+build       : r3.3.1_0
+build number: 0
+size        : 9.5 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.23.0-r3.3.1_0.tar.bz2
+md5         : d311d59408702abcc80c339d6ba17648
+dependencies: 
+  - r 3.3.1*
+
+
+bioconductor-rsubread 1.25.2 r3.3.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.25.2-r3.3.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.25.2
+build       : r3.3.1_0
+build number: 0
+size        : 9.5 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.3.1_0.tar.bz2
+md5         : 5c006c6d64894efd9a5e04e84ab381be
+dependencies: 
+  - r 3.3.1*
+
+
+bioconductor-rsubread 1.25.2 r3.3.2_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.25.2-r3.3.2_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.25.2
+build       : r3.3.2_0
+build number: 0
+size        : 9.5 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.3.2_0.tar.bz2
+md5         : 974a448e65f3ff585a9d657b103792bb
+dependencies: 
+  - r-base 3.3.2*
+
+
+bioconductor-rsubread 1.25.2 r3.4.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.25.2-r3.4.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.25.2
+build       : r3.4.1_0
+build number: 0
+size        : 9.5 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.25.2-r3.4.1_0.tar.bz2
+md5         : 454a7b15c5ee5492ef459771a53a59cc
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-rsubread 1.26.1 r3.4.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.26.1-r3.4.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.26.1
+build       : r3.4.1_0
+build number: 0
+size        : 9.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.26.1-r3.4.1_0.tar.bz2
+md5         : 53cfae394487d62425609df953e73189
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-rsubread 1.28.0 r3.4.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.28.0-r3.4.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.28.0
+build       : r3.4.1_0
+build number: 0
+size        : 9.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.28.0-r3.4.1_0.tar.bz2
+md5         : 3c66789af622cf84eadff1e5546446fe
+dependencies: 
+  - r-base 3.4.1*
+
+
+bioconductor-rsubread 1.28.1 r3.4.1_0
+-------------------------------------
+file name   : bioconductor-rsubread-1.28.1-r3.4.1_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.28.1
+build       : r3.4.1_0
+build number: 0
+size        : 9.6 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.28.1-r3.4.1_0.tar.bz2
+md5         : d6c5436fc825285e27c588572db16f03
+dependencies: 
+  - libgcc
+  - r-base 3.4.1*
+
+
+bioconductor-rsubread 1.30.9 r341h470a237_0
+-------------------------------------------
+file name   : bioconductor-rsubread-1.30.9-r341h470a237_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.30.9
+build       : r341h470a237_0
+build number: 0
+size        : 9.7 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.30.9-r341h470a237_0.tar.bz2
+md5         : c8612cb52fea959b5cdd938c00cadea6
+timestamp   : 2018-10-29 06:31:20 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.4.1,<3.4.2.0a0
+
+
+bioconductor-rsubread 1.30.9 r351h470a237_0
+-------------------------------------------
+file name   : bioconductor-rsubread-1.30.9-r351h470a237_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.30.9
+build       : r351h470a237_0
+build number: 0
+size        : 9.8 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.30.9-r351h470a237_0.tar.bz2
+md5         : 9f67ddc2689e32412ddf060994427c55
+timestamp   : 2018-10-29 06:30:05 UTC
+dependencies: 
+  - libgcc-ng >=4.9
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rsubread 1.32.2 r351h14c3975_0
+-------------------------------------------
+file name   : bioconductor-rsubread-1.32.2-r351h14c3975_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.32.2
+build       : r351h14c3975_0
+build number: 0
+size        : 9.8 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.32.2-r351h14c3975_0.tar.bz2
+md5         : 36a9250ffc898f64354e15e3656b7d32
+timestamp   : 2018-12-09 23:26:03 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rsubread 1.32.4 r351h14c3975_0
+-------------------------------------------
+file name   : bioconductor-rsubread-1.32.4-r351h14c3975_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.32.4
+build       : r351h14c3975_0
+build number: 0
+size        : 9.8 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.32.4-r351h14c3975_0.tar.bz2
+md5         : f7d00fe9379380fb0f9f138051ca2013
+timestamp   : 2019-04-24 04:19:33 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rsubread 1.34.0 r351h14c3975_0
+-------------------------------------------
+file name   : bioconductor-rsubread-1.34.0-r351h14c3975_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.34.0
+build       : r351h14c3975_0
+build number: 0
+size        : 11.0 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.34.0-r351h14c3975_0.tar.bz2
+md5         : 7e1f4c3d1a387aa8711ea08eee45251d
+timestamp   : 2019-05-08 07:53:29 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.5.1,<3.5.2.0a0
+
+
+bioconductor-rsubread 1.34.6 r36h516909a_0
+------------------------------------------
+file name   : bioconductor-rsubread-1.34.6-r36h516909a_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 1.34.6
+build       : r36h516909a_0
+build number: 0
+size        : 11.0 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-1.34.6-r36h516909a_0.tar.bz2
+md5         : 7070cd8d3f58aaff020f625ecfff2a0c
+timestamp   : 2019-07-23 06:25:39 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-rsubread 2.0.0 r36h516909a_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.0.0-r36h516909a_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.0.0
+build       : r36h516909a_0
+build number: 0
+size        : 11.0 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.0.0-r36h516909a_0.tar.bz2
+md5         : 7ba05406fb6ede09ac6d928a8001198c
+timestamp   : 2019-11-01 08:46:15 UTC
+dependencies: 
+  - libgcc-ng >=7.3.0
+  - r-base >=3.6,<3.7.0a0
+
+
+bioconductor-rsubread 2.2.1 r40h037d062_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.2.1-r40h037d062_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.2.1
+build       : r40h037d062_0
+build number: 0
+size        : 11.0 MB
+license     : GPL-3
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.2.1-r40h037d062_0.tar.bz2
+md5         : aeb0ba395c7b340b1e111b83ca03fdb7
+timestamp   : 2020-05-09 14:36:58 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.3.0
+  - liblapack >=3.8.0,<3.9.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-rsubread 2.4.0 r40h037d062_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.4.0-r40h037d062_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.4.0
+build       : r40h037d062_0
+build number: 0
+size        : 11.1 MB
+license     : GPL (>=3)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.4.0-r40h037d062_0.tar.bz2
+md5         : 3b237d29baf926c444724d4cc76a6f6a
+timestamp   : 2020-10-29 21:15:41 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=7.5.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-rsubread 2.4.3 r40hd029910_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.4.3-r40hd029910_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.4.3
+build       : r40hd029910_0
+build number: 0
+size        : 11.1 MB
+license     : GPL (>=3)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.4.3-r40hd029910_0.tar.bz2
+md5         : 70f557d34f5265abc2dada4d81cb3882
+timestamp   : 2021-03-26 08:00:29 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.0,<4.1.0a0
+  - r-matrix
+
+
+bioconductor-rsubread 2.6.1 r41hd029910_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.6.1-r41hd029910_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.6.1
+build       : r41hd029910_0
+build number: 0
+size        : 11.1 MB
+license     : GPL (>=3)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.6.1-r41hd029910_0.tar.bz2
+md5         : 633f020c3e4ac78de3929621a02dc286
+timestamp   : 2021-05-31 06:43:04 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.3.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-rsubread 2.8.0 r41hd029910_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.8.0-r41hd029910_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.8.0
+build       : r41hd029910_0
+build number: 0
+size        : 11.2 MB
+license     : GPL (>=3)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.8.0-r41hd029910_0.tar.bz2
+md5         : a0de89b4e3370b3c9179be60d55069c0
+timestamp   : 2021-11-01 17:01:35 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=9.4.0
+  - liblapack >=3.8.0,<4.0a0
+  - r-base >=4.1,<4.2.0a0
+  - r-matrix
+
+
+bioconductor-rsubread 2.8.1 r41h5c21468_0
+-----------------------------------------
+file name   : bioconductor-rsubread-2.8.1-r41h5c21468_0.tar.bz2
+name        : bioconductor-rsubread
+version     : 2.8.1
+build       : r41h5c21468_0
+build number: 0
+size        : 11.2 MB
+license     : GPL (>=3)
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-rsubread-2.8.1-r41h5c21468_0.tar.bz2
+md5         : 141bc9aee6b671f8785cf08d12aa32ee
+timestamp   : 2022-02-24 11:59:28 UTC
+dependencies: 
+  - libblas >=3.8.0,<4.0a0
+  - libgcc-ng >=10.3.0
+  - liblapack >=3.8.0,<

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-s4arrays.manual_bundle.txt

@@ -0,0 +1,226 @@
+# Tool: bioconductor-s4arrays
+software_name: bioconductor-s4arrays
+tier: T1
+domain: t1_backfill_overall
+downloads: 324254
+summary: Foundation of array-like containers in Bioconductor
+description: The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).
+dependencies: bioconductor-biocgenerics >=0.56.0,<0.57.0, bioconductor-biocgenerics >=0.56.0,<0.57.0a0, bioconductor-iranges >=2.44.0,<2.45.0, bioconductor-iranges >=2.44.0,<2.45.0a0, bioconductor-s4vectors >=0.48.0,<0.49.0, bioconductor-s4vectors >=0.48.0,<0.49.0a0, libblas >=3.9.0,<4.0a0, libgcc >=14, liblapack >=3.9.0,<4.0a0, liblzma >=5.8.2,<6.0a0, libzlib >=1.3.1,<2.0a0, r-abind, r-base >=4.5,<4.6.0a0, r-matrix
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.17/bioc/html/S4Arrays.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.17/bioc/html/S4Arrays.html
+Bioconductor - S4Arrays About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages S4Arrays S4Arrays This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see S4Arrays . Foundation of array-like containers in Bioconductor DOI: 10.18129/B9.bioc.S4Arrays Bioconductor version: 3.17 The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects). Author: Hervé Pagès [aut, cre] Maintainer: Hervé Pagès &#x3c;&#x68;&#x70;&#x61;&#x67;&#x65;&#x73;&#x2e;&#x6f;&#x6e;&#x2e;&#x67;&#x69;&#x74;&#x68;&#x75;&#x62;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("S4Arrays") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("S4Arrays") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("S4Arrays") A quick overview of the S4Arrays package HTML R Script Reference Manual PDF NEWS Text Need some help? Ask on the Bioconductor Support site! Details biocViews DataRepresentation , Infrastructure , Software Version 1.0.6 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License Artistic-2.0 Depends R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>= 0.45.2), S4Vectors , IRanges Imports stats, crayon System Requirements URL https://bioconductor.org/packages/S4Arrays Bug Reports https://github.com/Bioconductor/S4Arrays/issues See More Suggests BiocParallel , SparseArray (>= 0.0.4), DelayedArray , testthat, knitr, rmarkdown, BiocStyle Linking To S4Vectors Enhances Depends On Me DelayedArray , SparseArray Imports Me HDF5Array , SummarizedExperiment Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package S4Arrays_1.0.6.tar.gz Windows Binary S4Arrays_1.0.6.zip macOS Binary (x86_64) S4Arrays_1.0.6.tgz macOS Binary (arm64) S4Arrays_1.0.6.tgz Source Repository git clone https://git.bioconductor.org/packages/S4Arrays Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/S4Arrays Bioc Package Browser https://code.bioconductor.org/browse/S4Arrays/ Package Short Url https://bioconductor.org/packages/S4Arrays/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-s4arrays --info
+[rc=0]
+2 channel 
+Terms of 
+Service 
+accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-s4arrays 1.0.4 r43ha9d7317_0
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.0.4-r43ha9d7317_0.tar.bz2
+name        : bioconductor-s4arrays
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+build       : r43ha9d7317_0
+build number: 0
+size        : 785 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.0.4-r43ha9d7317_0.tar.bz2
+md5         : 53bb74ed857400d8ac101024cef98c7f
+timestamp   : 2023-07-10 19:52:18 UTC
+dependencies: 
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+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-base >=4.3,<4.4.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.2.0 r43ha9d7317_0
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.2.0-r43ha9d7317_0.tar.bz2
+name        : bioconductor-s4arrays
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+build number: 0
+size        : 797 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_0.tar.bz2
+md5         : 49bd3e143d591f9f57895cec0211f05a
+timestamp   : 2023-12-03 02:12:46 UTC
+dependencies: 
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+  - bioconductor-biocgenerics >=0.48.1,<1.0a0
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+  - bioconductor-iranges >=2.36.0,<3.0a0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-s4vectors >=0.40.2,<1.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-abind
+  - r-base >=4.3,<4.4.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.2.0 r43ha9d7317_1
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.2.0-r43ha9d7317_1.tar.bz2
+name        : bioconductor-s4arrays
+version     : 1.2.0
+build       : r43ha9d7317_1
+build number: 1
+size        : 795 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_1.tar.bz2
+md5         : c952b3c0a456fe9d00e4378b40a478f7
+timestamp   : 2023-12-06 04:55:03 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.48.0,<0.49.0
+  - bioconductor-biocgenerics >=0.48.1,<0.49.0a0
+  - bioconductor-iranges >=2.36.0,<2.37.0
+  - bioconductor-iranges >=2.36.0,<2.37.0a0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-s4vectors >=0.40.2,<0.41.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-abind
+  - r-base >=4.3,<4.4.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.2.0 r43ha9d7317_2
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.2.0-r43ha9d7317_2.tar.bz2
+name        : bioconductor-s4arrays
+version     : 1.2.0
+build       : r43ha9d7317_2
+build number: 2
+size        : 796 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.2.0-r43ha9d7317_2.tar.bz2
+md5         : 28fd3fe7fd8d087c1cfa7805bbd16661
+timestamp   : 2024-05-03 13:38:17 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.48.0,<0.49.0
+  - bioconductor-biocgenerics >=0.48.1,<0.49.0a0
+  - bioconductor-iranges >=2.36.0,<2.37.0
+  - bioconductor-iranges >=2.36.0,<2.37.0a0
+  - bioconductor-s4vectors >=0.40.0,<0.41.0
+  - bioconductor-s4vectors >=0.40.2,<0.41.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc-ng >=12
+  - liblapack >=3.9.0,<4.0a0
+  - r-abind
+  - r-base >=4.3,<4.4.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.6.0 r44h3df3fcb_0
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.6.0-r44h3df3fcb_0.tar.bz2
+name        : bioconductor-s4arrays
+version     : 1.6.0
+build       : r44h3df3fcb_0
+build number: 0
+size        : 1.0 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.6.0-r44h3df3fcb_0.tar.bz2
+md5         : 321539e20f732857eeda26f9ec5c9d9d
+timestamp   : 2024-12-18 23:54:18 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.52.0,<0.53.0
+  - bioconductor-biocgenerics >=0.52.0,<0.53.0a0
+  - bioconductor-iranges >=2.40.0,<2.41.0
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+  - bioconductor-s4vectors >=0.44.0,<0.45.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - r-abind
+  - r-base >=4.4,<4.5.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.6.0 r44h3df3fcb_1
+-----------------------------------------
+file name   : bioconductor-s4arrays-1.6.0-r44h3df3fcb_1.tar.bz2
+name        : bioconductor-s4arrays
+version     : 1.6.0
+build       : r44h3df3fcb_1
+build number: 1
+size        : 1.0 MB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.6.0-r44h3df3fcb_1.tar.bz2
+md5         : a6774527b21da1eb7a99b3839301ab57
+timestamp   : 2025-04-14 20:33:09 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.52.0,<0.53.0
+  - bioconductor-biocgenerics >=0.52.0,<0.53.0a0
+  - bioconductor-iranges >=2.40.0,<2.41.0
+  - bioconductor-iranges >=2.40.0,<2.41.0a0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0
+  - bioconductor-s4vectors >=0.44.0,<0.45.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=13
+  - liblapack >=3.9.0,<4.0a0
+  - r-abind
+  - r-base >=4.4,<4.5.0a0
+  - r-crayon
+  - r-matrix
+
+
+bioconductor-s4arrays 1.10.1 r45h01b2380_0
+------------------------------------------
+file name   : bioconductor-s4arrays-1.10.1-r45h01b2380_0.conda
+name        : bioconductor-s4arrays
+version     : 1.10.1
+build       : r45h01b2380_0
+build number: 0
+size        : 1003 KB
+license     : Artistic-2.0
+subdir      : linux-64
+url         : https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4arrays-1.10.1-r45h01b2380_0.conda
+md5         : 0b2ad083cc4002a36926c7c31be1c5c8
+timestamp   : 2026-02-09 09:10:51 UTC
+dependencies: 
+  - bioconductor-biocgenerics >=0.56.0,<0.57.0
+  - bioconductor-biocgenerics >=0.56.0,<0.57.0a0
+  - bioconductor-iranges >=2.44.0,<2.45.0
+  - bioconductor-iranges >=2.44.0,<2.45.0a0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0
+  - bioconductor-s4vectors >=0.48.0,<0.49.0a0
+  - libblas >=3.9.0,<4.0a0
+  - libgcc >=14
+  - liblapack >=3.9.0,<4.0a0
+  - liblzma >=5.8.2,<6.0a0
+  - libzlib >=1.3.1,<2.0a0
+  - r-abind
+  - r-base >=4.5,<4.6.0a0
+  - r-matrix

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scannotatr.manual_bundle.txt

@@ -0,0 +1,203 @@
+# Tool: bioconductor-scannotatr
+software_name: bioconductor-scannotatr
+tier: T1
+domain: single_cell
+downloads: 8244
+summary: Pretrained learning models for cell type prediction on single cell RNA-sequencing data
+description: The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.
+dependencies: bioconductor-annotationhub >=4.0.0,<4.1.0, bioconductor-singlecellexperiment >=1.32.0,<1.33.0, bioconductor-summarizedexperiment >=1.40.0,<1.41.0, r-ape, r-base >=4.5,<4.6.0a0, r-caret, r-data.tree, r-dplyr, r-e1071, r-ggplot2, r-kernlab, r-proc, r-rocr, r-seurat
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.14/bioc/html/scAnnotatR.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.14/bioc/html/scAnnotatR.html
+Bioconductor - scAnnotatR About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.14 Software Packages scAnnotatR scAnnotatR This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see scAnnotatR . Pretrained learning models for cell type prediction on single cell RNA-sequencing data DOI: 10.18129/B9.bioc.scAnnotatR Bioconductor version: 3.14 The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs. Author: Vy Nguyen [aut] , Johannes Griss [cre] Maintainer: Johannes Griss &#x3c;&#x6a;&#x6f;&#x68;&#x61;&#x6e;&#x6e;&#x65;&#x73;&#x2e;&#x67;&#x72;&#x69;&#x73;&#x73;&#x20;&#x61;&#x74;&#x20;&#x6d;&#x65;&#x64;&#x75;&#x6e;&#x69;&#x77;&#x69;&#x65;&#x6e;&#x2e;&#x61;&#x63;&#x2e;&#x61;&#x74;&#x3e; Citation (from within R, enter citation("scAnnotatR") ): Installation To install this package, start R (version "4.1") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scAnnotatR") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scAnnotatR") 1. Introduction to scAnnotatR HTML R Script 2. Training basic model HTML R Script 3. Training child model HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Classification , GeneExpression , SingleCell , Software , SupportVectorMachine , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.14 (R-4.1) (2.5 years) License MIT + file LICENSE Depends R (>= 4.1), Seurat, SingleCellExperiment , SummarizedExperiment Imports dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub , utils System Requirements URL https://github.com/grisslab/scAnnotatR Bug Reports https://github.com/grisslab/scAnnotatR/issues/new See More Suggests knitr, rmarkdown, scRNAseq , testthat Linking To Enhances Depends On Me Imports Me Suggests Me scAnnotatR.models Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scAnnotatR_1.0.0.tar.gz Windows Binary scAnnotatR_1.0.0.zip macOS 10.13 (High Sierra) scAnnotatR_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scAnnotatR Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scAnnotatR Bioc Package Browser https://code.bioconductor.org/browse/scAnnotatR/ Package Short Url https://bioconductor.org/packages/scAnnotatR/ Package Downloads Report Download Stats Old Source Packages for BioC 3.14 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-scannotatr --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ done
+bioconductor-scannotatr 1.0.0 r41hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scannotatr-1.0.0-r41hdfd78af_0.tar.bz2
+name        : bioconductor-scannotatr
+version     : 1.0.0
+build       : r41hdfd78af_0
+build number: 0
+size        : 1.1 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.0.0-r41hdfd78af_0.tar.bz2
+md5         : 520a655cbf1037ead332fca8c41c65a6
+timestamp   : 2021-11-06 23:51:31 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.2.0,<3.3.0
+  - bioconductor-singlecellexperiment >=1.16.0,<1.17.0
+  - bioconductor-summarizedexperiment >=1.24.0,<1.25.0
+  - r-ape
+  - r-base >=4.1,<4.2.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat
+
+
+bioconductor-scannotatr 1.4.0 r42hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scannotatr-1.4.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-scannotatr
+version     : 1.4.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 1.2 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.4.0-r42hdfd78af_0.tar.bz2
+md5         : d5156f24420bc2f8a5cd77f7f070cee6
+timestamp   : 2022-11-08 01:15:21 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.6.0,<3.7.0
+  - bioconductor-singlecellexperiment >=1.20.0,<1.21.0
+  - bioconductor-summarizedexperiment >=1.28.0,<1.29.0
+  - r-ape
+  - r-base >=4.2,<4.3.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat
+
+
+bioconductor-scannotatr 1.6.0 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scannotatr-1.6.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scannotatr
+version     : 1.6.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 986 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.6.0-r43hdfd78af_0.tar.bz2
+md5         : 87395666ef511874ed387f9f2c548d4f
+timestamp   : 2023-07-13 11:03:33 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.8.0,<3.9.0
+  - bioconductor-singlecellexperiment >=1.22.0,<1.23.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat
+
+
+bioconductor-scannotatr 1.8.0 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scannotatr-1.8.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scannotatr
+version     : 1.8.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 983 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.8.0-r43hdfd78af_0.tar.bz2
+md5         : 28ed4744724229c7a1f830d92fdf1951
+timestamp   : 2023-12-06 23:00:06 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.10.0,<3.11.0
+  - bioconductor-singlecellexperiment >=1.24.0,<1.25.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat
+
+
+bioconductor-scannotatr 1.12.0 r44hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-scannotatr-1.12.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-scannotatr
+version     : 1.12.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 1.0 MB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.12.0-r44hdfd78af_0.tar.bz2
+md5         : 4f75fb4bb59eba9320090d9f427983ae
+timestamp   : 2025-01-04 03:20:24 UTC
+dependencies: 
+  - bioconductor-annotationhub >=3.14.0,<3.15.0
+  - bioconductor-singlecellexperiment >=1.28.0,<1.29.0
+  - bioconductor-summarizedexperiment >=1.36.0,<1.37.0
+  - r-ape
+  - r-base >=4.4,<4.5.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat
+
+
+bioconductor-scannotatr 1.16.0 r45hdfd78af_0
+--------------------------------------------
+file name   : bioconductor-scannotatr-1.16.0-r45hdfd78af_0.conda
+name        : bioconductor-scannotatr
+version     : 1.16.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 940 KB
+license     : MIT + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scannotatr-1.16.0-r45hdfd78af_0.conda
+md5         : fe588d26acba6000fe3f92b5596b4110
+timestamp   : 2026-03-01 13:26:25 UTC
+dependencies: 
+  - bioconductor-annotationhub >=4.0.0,<4.1.0
+  - bioconductor-singlecellexperiment >=1.32.0,<1.33.0
+  - bioconductor-summarizedexperiment >=1.40.0,<1.41.0
+  - r-ape
+  - r-base >=4.5,<4.6.0a0
+  - r-caret
+  - r-data.tree
+  - r-dplyr
+  - r-e1071
+  - r-ggplot2
+  - r-kernlab
+  - r-proc
+  - r-rocr
+  - r-seurat

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scbubbletree.manual_bundle.txt

@@ -0,0 +1,157 @@
+# Tool: bioconductor-scbubbletree
+software_name: bioconductor-scbubbletree
+tier: T1
+domain: single_cell
+downloads: 4317
+summary: Quantitative visual exploration of scRNA-seq data
+description: scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.
+dependencies: bioconductor-biocparallel >=1.44.0,<1.45.0, bioconductor-ggtree >=4.0.0,<4.1.0, r-ape, r-base >=4.5,<4.6.0a0, r-dplyr, r-ggplot2, r-patchwork, r-proxy, r-reshape2, r-scales, r-seurat
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.16/bioc/html/scBubbletree.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.16/bioc/html/scBubbletree.html
+Bioconductor - scBubbletree About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.16 Software Packages scBubbletree scBubbletree This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see scBubbletree . Quantitative visual exploration of scRNA-seq data DOI: 10.18129/B9.bioc.scBubbletree Bioconductor version: 3.16 scBubbletree is a quantitative method for visual exploration of scRNA-seq data. It preserves biologically meaningful properties of scRNA-seq data, such as local and global cell distances, as well as the density distribution of cells across the sample. scBubbletree is scalable and avoids the overplotting problem, and is able to visualize diverse cell attributes derived from multiomic single-cell experiments. Importantly, Importantly, scBubbletree is easy to use and to integrate with popular approaches for scRNA-seq data analysis. Author: Simo Kitanovski [aut, cre] Maintainer: Simo Kitanovski &#x3c;&#x73;&#x69;&#x6d;&#x6f;&#x6b;&#x69;&#x74;&#x61;&#x6e;&#x6f;&#x76;&#x73;&#x6b;&#x69;&#x20;&#x61;&#x74;&#x20;&#x67;&#x6d;&#x61;&#x69;&#x6c;&#x2e;&#x63;&#x6f;&#x6d;&#x3e; Citation (from within R, enter citation("scBubbletree") ): Installation To install this package, start R (version "4.2") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scBubbletree") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scBubbletree") User Manual: scBubbletree HTML R Script Reference Manual PDF NEWS Text LICENSE Text Need some help? Ask on the Bioconductor Support site! Details biocViews Clustering , RNASeq , SingleCell , Software , Transcriptomics , Visualization Version 1.0.0 In Bioconductor since BioC 3.16 (R-4.2) (1.5 years) License GPL-3 + file LICENSE Depends R (>= 4.2.0) Imports reshape2, future, future.apply, ape, scales, Seurat, ggplot2, ggtree , patchwork, methods, stats, base, utils System Requirements Python (>= 3.6), leidenalg (>= 0.8.2) URL https://github.com/snaketron/scBubbletree Bug Reports https://github.com/snaketron/scBubbletree/issues See More Suggests BiocStyle , knitr, testthat, cluster, SingleCellExperiment Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scBubbletree_1.0.0.tar.gz Windows Binary scBubbletree_1.0.0.zip macOS Binary (x86_64) scBubbletree_1.0.0.tgz macOS Binary (arm64) scBubbletree_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scBubbletree Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scBubbletree Bioc Package Browser https://code.bioconductor.org/browse/scBubbletree/ Package Short Url https://bioconductor.org/packages/scBubbletree/ Package Downloads Report Download Stats Old Source Packages for BioC 3.16 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-scbubbletree --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | done
+bioconductor-scbubbletree 1.0.0 r42hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-scbubbletree-1.0.0-r42hdfd78af_0.tar.bz2
+name        : bioconductor-scbubbletree
+version     : 1.0.0
+build       : r42hdfd78af_0
+build number: 0
+size        : 2.3 MB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.0.0-r42hdfd78af_0.tar.bz2
+md5         : 00cbfef68aacff3c7dde5c5f9ac23556
+timestamp   : 2022-11-03 11:43:06 UTC
+dependencies: 
+  - bioconductor-ggtree >=3.6.0,<3.7.0
+  - r-ape
+  - r-base >=4.2,<4.3.0a0
+  - r-future
+  - r-future.apply
+  - r-ggplot2
+  - r-patchwork
+  - r-reshape2
+  - r-scales
+  - r-seurat
+
+
+bioconductor-scbubbletree 1.2.0 r43hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-scbubbletree-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scbubbletree
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 2.3 MB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : 909b65b3865909f6955e4349c0096718
+timestamp   : 2023-07-07 16:23:12 UTC
+dependencies: 
+  - bioconductor-ggtree >=3.8.0,<3.9.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-future
+  - r-future.apply
+  - r-ggplot2
+  - r-patchwork
+  - r-proxy
+  - r-reshape2
+  - r-scales
+  - r-seurat
+
+
+bioconductor-scbubbletree 1.4.0 r43hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-scbubbletree-1.4.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scbubbletree
+version     : 1.4.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 2.3 MB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.4.0-r43hdfd78af_0.tar.bz2
+md5         : db6faa909e6a47b4fc6f9ebe63f4bc98
+timestamp   : 2023-12-04 21:16:44 UTC
+dependencies: 
+  - bioconductor-ggtree >=3.10.0,<3.11.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-future
+  - r-future.apply
+  - r-ggplot2
+  - r-patchwork
+  - r-proxy
+  - r-reshape2
+  - r-scales
+  - r-seurat
+
+
+bioconductor-scbubbletree 1.8.0 r44hdfd78af_0
+---------------------------------------------
+file name   : bioconductor-scbubbletree-1.8.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-scbubbletree
+version     : 1.8.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 2.9 MB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.8.0-r44hdfd78af_0.tar.bz2
+md5         : ec39386c93cb499570c1f4cbf58fd1be
+timestamp   : 2024-12-15 01:58:05 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-ggtree >=3.14.0,<3.15.0
+  - r-ape
+  - r-base >=4.4,<4.5.0a0
+  - r-dplyr
+  - r-ggplot2
+  - r-patchwork
+  - r-proxy
+  - r-reshape2
+  - r-scales
+  - r-seurat
+
+
+bioconductor-scbubbletree 1.12.0 r45hdfd78af_0
+----------------------------------------------
+file name   : bioconductor-scbubbletree-1.12.0-r45hdfd78af_0.conda
+name        : bioconductor-scbubbletree
+version     : 1.12.0
+build       : r45hdfd78af_0
+build number: 0
+size        : 2.8 MB
+license     : GPL-3 + file LICENSE
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scbubbletree-1.12.0-r45hdfd78af_0.conda
+md5         : 5f20528d389efe621f8c7e7dd608058c
+timestamp   : 2026-02-08 20:37:25 UTC
+dependencies: 
+  - bioconductor-biocparallel >=1.44.0,<1.45.0
+  - bioconductor-ggtree >=4.0.0,<4.1.0
+  - r-ape
+  - r-base >=4.5,<4.6.0a0
+  - r-dplyr
+  - r-ggplot2
+  - r-patchwork
+  - r-proxy
+  - r-reshape2
+  - r-scales
+  - r-seurat

BioScientist/agent_system/toolbase/output/help_docs/manual_bundle_txt/bioconductor-scfeatures.manual_bundle.txt

@@ -0,0 +1,150 @@
+# Tool: bioconductor-scfeatures
+software_name: bioconductor-scfeatures
+tier: T1
+domain: single_cell
+downloads: 3092
+summary: scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
+description: scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.
+dependencies: bioconductor-aucell >=1.28.0,<1.29.0, bioconductor-biocparallel >=1.40.0,<1.41.0, bioconductor-delayedarray >=0.32.0,<0.33.0, bioconductor-delayedmatrixstats >=1.28.0,<1.29.0, bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0, bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0, bioconductor-ensembldb >=2.30.0,<2.31.0, bioconductor-gsva >=2.0.0,<2.1.0, bioconductor-matrixgenerics >=1.18.0,<1.19.0, bioconductor-singlecellsignalr >=1.18.0,<1.19.0, r-ape, r-base >=4.4,<4.5.0a0, r-cli, r-dplyr, r-dt, r-glue, r-gtools, r-msigdbr, r-proxyc, r-reshape2, r-rmarkdown, r-seurat, r-spatstat.explore, r-spatstat.geom, r-tidyr
+execution_environment: R
+execution_environment_reason: inferred from package/dependencies (R ecosystem)
+
+## URLs
+home_url: https://bioconductor.org/packages/3.17/bioc/html/scFeatures.html
+doc_url: 
+dev_url: 
+
+## URL Docs Extract
+### https://bioconductor.org/packages/3.17/bioc/html/scFeatures.html
+Bioconductor - scFeatures About Learn Packages Developers Search Get Started Menu Home Bioconductor 3.17 Software Packages scFeatures scFeatures This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see scFeatures . scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction DOI: 10.18129/B9.bioc.scFeatures Bioconductor version: 3.17 scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor. Author: Yue Cao [aut, cre], Yingxin Lin [aut], Ellis Patrick [aut], Pengyi Yang [aut], Jean Yee Hwa Yang [aut] Maintainer: Yue Cao &#x3c;&#x79;&#x75;&#x65;&#x2e;&#x63;&#x61;&#x6f;&#x20;&#x61;&#x74;&#x20;&#x73;&#x79;&#x64;&#x6e;&#x65;&#x79;&#x2e;&#x65;&#x64;&#x75;&#x2e;&#x61;&#x75;&#x3e; Citation (from within R, enter citation("scFeatures") ): Installation To install this package, start R (version "4.3") and enter: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scFeatures") For older versions of R, please refer to the appropriate Bioconductor release . Documentation To view documentation for the version of this package installed in your system, start R and enter: browseVignettes("scFeatures") Overview of scFeatures with case studies HTML R Script Reference Manual PDF Need some help? Ask on the Bioconductor Support site! Details biocViews CellBasedAssays , SingleCell , Software , Spatial , Transcriptomics Version 1.0.0 In Bioconductor since BioC 3.17 (R-4.3) (1 year) License GPL-3 Depends R (>= 4.2.0) Imports DelayedArray , DelayedMatrixStats , EnsDb.Hsapiens.v79 , EnsDb.Mmusculus.v79 , GSVA , Seurat, ape, glue, dplyr, ensembldb , gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell , BiocParallel , SpatialExperiment , SummarizedExperiment , rmarkdown, methods, stats, DT, cli, SingleCellSignalR , MatrixGenerics System Requirements URL Bug Reports https://github.com/SydneyBioX/scFeatures/issues See More Suggests knitr, S4Vectors , survival, survminer, BiocStyle , ClassifyR , org.Hs.eg.db , clusterProfiler Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives Follow Installation instructions to use this package in your R session. Source Package scFeatures_1.0.0.tar.gz Windows Binary scFeatures_1.0.0.zip macOS Binary (x86_64) scFeatures_1.0.0.tgz macOS Binary (arm64) scFeatures_1.0.0.tgz Source Repository git clone https://git.bioconductor.org/packages/scFeatures Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scFeatures Bioc Package Browser https://code.bioconductor.org/browse/scFeatures/ Package Short Url https://bioconductor.org/packages/scFeatures/ Package Downloads Report Download Stats Old Source Packages for BioC 3.17 Source Archive About Annual Reports Collaborations Core Team Mirrors Dashboard Project Details Code of Conduct Developers Package Guidelines Package Submission Release Schedule Release Announcements Source Control Browsable Code Base Build Reports Learn Education and Training Bioconductor Books Package Vignettes Workflows Publications Community Resources Get Help Get started Install R Find Bioconductor Packages Install Bioconductor Packages Update Bioconductor Packages Docker Images Bioconductor in AnVIL Bioconductor Packages Contact us: support.bioconductor.org Copyright &copy; 2003 - 2024 Bioconductor
+
+## Conda Search Info
+$ conda search -c bioconda -c conda-forge bioconductor-scfeatures --info
+[rc=0]
+2 channel Terms of Service accepted
+Loading channels: - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - done
+bioconductor-scfeatures 1.0.0 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scfeatures-1.0.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scfeatures
+version     : 1.0.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 3.2 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.0.0-r43hdfd78af_0.tar.bz2
+md5         : 2dc063889e0849feb1b76ac37b727a4e
+timestamp   : 2023-07-19 11:49:57 UTC
+dependencies: 
+  - bioconductor-aucell >=1.22.0,<1.23.0
+  - bioconductor-biocparallel >=1.34.0,<1.35.0
+  - bioconductor-delayedarray >=0.26.0,<0.27.0
+  - bioconductor-delayedmatrixstats >=1.22.0,<1.23.0
+  - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensembldb >=2.24.0,<2.25.0
+  - bioconductor-gsva >=1.48.0,<1.49.0
+  - bioconductor-matrixgenerics >=1.12.0,<1.13.0
+  - bioconductor-singlecellsignalr >=1.12.0,<1.13.0
+  - bioconductor-spatialexperiment >=1.10.0,<1.11.0
+  - bioconductor-summarizedexperiment >=1.30.0,<1.31.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-cli
+  - r-dplyr
+  - r-dt
+  - r-glue
+  - r-gtools
+  - r-msigdbr
+  - r-proxyc
+  - r-reshape2
+  - r-rmarkdown
+  - r-seurat
+  - r-spatstat.explore
+  - r-spatstat.geom
+  - r-tidyr
+
+
+bioconductor-scfeatures 1.2.0 r43hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scfeatures-1.2.0-r43hdfd78af_0.tar.bz2
+name        : bioconductor-scfeatures
+version     : 1.2.0
+build       : r43hdfd78af_0
+build number: 0
+size        : 3.2 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.2.0-r43hdfd78af_0.tar.bz2
+md5         : 4ae2a029c905467547a7ec7eee0dcec7
+timestamp   : 2023-12-19 18:08:04 UTC
+dependencies: 
+  - bioconductor-aucell >=1.24.0,<1.25.0
+  - bioconductor-biocparallel >=1.36.0,<1.37.0
+  - bioconductor-delayedarray >=0.28.0,<0.29.0
+  - bioconductor-delayedmatrixstats >=1.24.0,<1.25.0
+  - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensembldb >=2.26.0,<2.27.0
+  - bioconductor-gsva >=1.50.0,<1.51.0
+  - bioconductor-matrixgenerics >=1.14.0,<1.15.0
+  - bioconductor-singlecellsignalr >=1.14.0,<1.15.0
+  - bioconductor-spatialexperiment >=1.12.0,<1.13.0
+  - bioconductor-summarizedexperiment >=1.32.0,<1.33.0
+  - r-ape
+  - r-base >=4.3,<4.4.0a0
+  - r-cli
+  - r-dplyr
+  - r-dt
+  - r-glue
+  - r-gtools
+  - r-msigdbr
+  - r-proxyc
+  - r-reshape2
+  - r-rmarkdown
+  - r-seurat
+  - r-spatstat.explore
+  - r-spatstat.geom
+  - r-tidyr
+
+
+bioconductor-scfeatures 1.6.0 r44hdfd78af_0
+-------------------------------------------
+file name   : bioconductor-scfeatures-1.6.0-r44hdfd78af_0.tar.bz2
+name        : bioconductor-scfeatures
+version     : 1.6.0
+build       : r44hdfd78af_0
+build number: 0
+size        : 3.2 MB
+license     : GPL-3
+subdir      : noarch
+url         : https://conda.anaconda.org/bioconda/noarch/bioconductor-scfeatures-1.6.0-r44hdfd78af_0.tar.bz2
+md5         : f378e7ede0ececa75394acdf3e7d54b8
+timestamp   : 2025-01-05 05:38:06 UTC
+dependencies: 
+  - bioconductor-aucell >=1.28.0,<1.29.0
+  - bioconductor-biocparallel >=1.40.0,<1.41.0
+  - bioconductor-delayedarray >=0.32.0,<0.33.0
+  - bioconductor-delayedmatrixstats >=1.28.0,<1.29.0
+  - bioconductor-ensdb.hsapiens.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensdb.mmusculus.v79 >=2.99.0,<2.100.0
+  - bioconductor-ensembldb >=2.30.0,<2.31.0
+  - bioconductor-gsva >=2.0.0,<2.1.0
+  - bioconductor-matrixgenerics >=1.18.0,<1.19.0
+  - bioconductor-singlecellsignalr >=1.18.0,<1.19.0
+  - r-ape
+  - r-base >=4.4,<4.5.0a0
+  - r-cli
+  - r-dplyr
+  - r-dt
+  - r-glue
+  - r-gtools
+  - r-msigdbr
+  - r-proxyc
+  - r-reshape2
+  - r-rmarkdown
+  - r-seurat
+  - r-spatstat.explore
+  - r-spatstat.geom
+  - r-tidyr