---
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/)