File size: 3,023 Bytes
a736456 0de850a a736456 0de850a a736456 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 | ---
license: mit
---
# PiperNET data
Data for PiperNET, a multi-*omics* platform for elucidating the biosynthetic origin of plant specialized metabolites.
It holds LC-MS metabolomics and RNA-Seq transcriptomics data from several *Piper* species and tissues, with biological replicates.
Code and pipeline: [github.com/titodamiani/PiperNET](https://github.com/titodamiani/PiperNET).
## Download
With the [`hf` command line tool](https://huggingface.co/docs/huggingface_hub/guides/cli):
```bash
hf download titodamiani/PiperNET --repo-type dataset --local-dir data
```
To download one folder only, add `--include`, for example `--include "processed/*"`.
To run the code on this data, follow the installation steps in the [code repository](https://github.com/titodamiani/PiperNET).
## Structure
```
data/
├── README.md # this dataset card
├── raw/
│ ├── lcms/
│ │ ├── rawfiles/ # LC-MS raw files, mzML (140 files)
│ │ └── metadata.tsv # sample metadata, read by MZmine
│ └── rnaseq/piperNN/ # transXpress output, one folder per sample ID (13)
│ ├── transcriptome.fasta # de novo assembly
│ ├── transcriptome.pep # predicted proteins
│ ├── transcriptome_expression_isoform.tsv
│ ├── busco_report.txt
│ └── annotations/ # Pfam, BLASTp, SignalP, TargetP, TMHMM
├── interim/
│ ├── lcms_mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml)
│ └── rnaseq_clstr/piperNN/ # CD-HIT clustered proteomes
├── external/
│ ├── molecular_networks/
│ │ └── gnps2/ # GNPS2 feature-based molecular networking results
│ ├── sirius/ # SIRIUS results: CSI:FingerID structures, CANOPUS classes
│ ├── orthogroups/sonicpd/ # SonicParanoid orthogroups
│ ├── speclibs/ # MS/MS spectral libraries for annotation in MZmine
│ ├── known_enzymes/ # known enzymes table
│ ├── customDB.csv # manually curated list of known LC-MS features, for targeted feature detection in MZmine
│ ├── standardDB.csv # read by MZmine and the LC-MS data preparation
│ └── novelty_scores.csv # preliminary
└── processed/
├── ftable_clean.csv # LC-MS feature table
├── ntable_clean.csv # GNPS2 node table, for Cytoscape
├── proteomes/piperNN/ # proteome.pep, proteome.csv, blastDB/
├── proteomes_all.csv # all proteomes with orthogroups
└── scoring/ # input arrays for network-orthogroup scoring (.npy)
```
`scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made.
|