| --- |
| 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 |
| ├── interim/ |
| │ ├── mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml) |
| │ ├── transxpress/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 |
| │ └── cdhit/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 |
| Column and ID conventions: [docs/data.md](https://github.com/titodamiani/PiperNET/blob/master/docs/data.md). |
|
|
| `scripts/README.md` in the [code repository](https://github.com/titodamiani/PiperNET) describes how each file is made. |
|
|
