Skills

A skill is a package of structured files that teaches an AI coding agent how to work with a specific tool or framework. The skill below was generated by Great Docs from this project’s documentation. Install it in your agent and it will be able to run commands, edit configuration, write content, and troubleshoot problems without step-by-step guidance from you.

Any agent — install with npx:

npx skills add pelingundogdu/sigpathmatrix

Codex / OpenCode

Tell the agent:
Fetch the skill file from https://github.com/pelingundogdu/sigpathmatrix and follow the instructions.

Manual — download the skill file:

curl -O <site-url>/skill.md

Or browse the SKILL.md file.

SKILL.md

---
name: sigpathmatrix
description: >
  The default prior biological knowledge using in sigPrimedNet network. Use when writing Python code that uses the sigpathmatrix package.
license: GPL-3.0-or-later
compatibility: Requires Python >=3.12.
---

# sigpathmatrix

The default prior biological knowledge using in sigPrimedNet network

## Installation

```bash
pip install sigpathmatrix
```

## API overview

### Classes

Main classes provided by the package

- `path_manager.ProjectPaths`

### Functions

Utility functions

- `collect_bio_layer.collect_hipathia_pathway`
- `collect_bio_layer.create_pbk_matrix_hipathia_signaling`
- `collect_bio_layer.remove_disease_pathways`
- `default_pbk_hipathia.convert_custom_list_into_list`
- `default_pbk_hipathia.main`
- `default_pbk_hipathia.process_default_pbk`
- `package_env_manager.check_env_line_exist`
- `package_env_manager.load_dependencies`
- `py_collect_gene_entrezid.py_gene_from_hipathia`
- `py_collect_gene_entrezid.py_gene_id_entrez_converter`
- `run_dependency.main`
- `run_dependency.run_dependency_installer`
- `run_dependency.setup_project_env`
- `spn_config.setup_project`

### Constants

Module-level constants and data

- `spn_config.DATA_SPN_HELPER_DIR`
- `spn_config.DISEASE_KEYWORD`
- `spn_config.DISEASE_LIST`
- `spn_config.GA_DICT`
- `spn_config.PROCESSED_DIR`
- `spn_config.RAW_DIR`

## Resources

- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs
- [Source code](https://github.com/pelingundogdu/sigpathmatrix/)