Add OrthoFinder orthogroups, rename orthogroup columns, update piper25 and processed files
61430c8 verified | 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 and the genes in no orthogroup | |
| │ │ └── orthofinder/ # OrthoFinder orthogroups, MCL clusters, species tree and run log | |
| │ ├── 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 SonicParanoid and OrthoFinder orthogroups | |
| ``` | |
| ## IDs | |
| - `ftable_clean.csv` and `ntable_clean.csv`: `network_id` > 0 is a molecular network. A singleton feature is its own network, with `network_id` = -`feat_id`. | |
| - `proteomes_all.csv`: 4 columns per orthogroup tool, with the prefix `sonicpd_` (SonicParanoid) or `orthofinder_` (OrthoFinder): `_id`, `_size` (genes), `_sp_in_grp` (species), `_intersp` (species joined with `;`). | |
| - A singleton transcript is its own orthogroup, with a negative ID (-1, -2, ...). `sonicpd_id` starts at 1. `orthofinder_id` is the number in the OrthoFinder ID (`OG0000123` is 123), so it starts at 0. | |
| `scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made. | |