### Get Help for PTM-SEA Command Line Interface

Source: https://github.com/broadinstitute/ssgsea2.0/blob/master/Readme.md

This command retrieves usage instructions and available options for the `ssgsea-cli.R` script. This script is recommended for integrating PTM-SEA into automated analysis pipelines and has been tested across Windows, Mac, and Linux operating systems.

```bash
ssgsea-cli.R --help
```

--------------------------------

### Get Help for GCT Preprocessing Command Line Tool

Source: https://github.com/broadinstitute/ssgsea2.0/blob/master/Readme.md

This command provides detailed instructions for using the `preprocess_gct-cli.R` script. This utility is crucial for converting GCT file row IDs (e.g., UniProt, RefSeq, gene symbol) into the specific UniProt and 7AA flanking sequence format required by PTM-SEA for site identification.

```bash
preprocess_gct-cli.R --help
```

--------------------------------

### PTMsigDB Site Identifier Formats and Data Download

Source: https://github.com/broadinstitute/ssgsea2.0/blob/master/Readme.md

This section outlines the three primary identifier formats used in PTMsigDB for phosphorylation sites: UniProt-centric, Flanking sequence, and PSP site group ID. It provides examples for how these identifiers appear within PTMsigDB and how they should be formatted for compatibility with external datasets. Additionally, direct download links are provided for human, mouse, and rat datasets in GMT format for each identifier type. The direction of change (up/down-regulation) is a PTMsigDB-specific annotation and should be omitted when preparing dataset identifiers.

```APIDOC
Database format: UniProt-centric
  Site accession: Uniprot_acc;site-type;direction
  Example in PTMsigDB: Q06609;Y315-p;u
  Example in dataset: Q06609;Y315-p
  Download:
    human: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.uniprot.human.v2.0.0.gmt
    mouse: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.uniprot.mouse.v2.0.0.gmt
    rat: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.uniprot.rat.v2.0.0.gmt

Database format: Flanking sequence
  Site accession: +/-7aa flanking seq-type;direction
  Example in PTMsigDB: ETRICKIYDSPCLPE-p;u
  Example in dataset: ETRICKIYDSPCLPE-p
  Download:
    human: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.flanking.human.v2.0.0.gmt
    mouse: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.flanking.mouse.v2.0.0.gmt
    rat: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.flanking.rat.v2.0.0.gmt

Database format: PSP site group id
  Site accession: site_grp_id-type;direction
  Example in PTMsigDB: 448324-p;u
  Example in dataset: 448324-p
  Download:
    human: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.sitegrpid.human.v2.0.0.gmt
    mouse: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.sitegrpid.mouse.v2.0.0.gmt
    rat: https://raw.githubusercontent.com/broadinstitute/ssGSEA2.0/master/db/ptmsigdb/v2.0.0/all/ptm.sig.db.all.sitegrpid.rat.v2.0.0.gmt

Note: The direction of change for a PTM site in a signature is indicated by ;u (up-regulation) or ;d (down-regulation). This annotation is a feature of PTMsigDB and must not be included when generating compatible site identifiers for a particular dataset.
```

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