# sigpathmatrix

> The default prior biological knowledge using in sigPrimedNet network

## Docs

### API Reference

#### Classes
> Main classes provided by the package

- [path_manager.ProjectPaths](reference/path_manager.ProjectPaths.html)

#### Functions
> Utility functions

- [collect_bio_layer.collect_hipathia_pathway](reference/collect_bio_layer.collect_hipathia_pathway.html)
- [collect_bio_layer.create_pbk_matrix_hipathia_signaling](reference/collect_bio_layer.create_pbk_matrix_hipathia_signaling.html)
- [collect_bio_layer.remove_disease_pathways](reference/collect_bio_layer.remove_disease_pathways.html)
- [default_pbk_hipathia.convert_custom_list_into_list](reference/default_pbk_hipathia.convert_custom_list_into_list.html)
- [default_pbk_hipathia.main](reference/default_pbk_hipathia.main.html)
- [default_pbk_hipathia.process_default_pbk](reference/default_pbk_hipathia.process_default_pbk.html)
- [package_env_manager.check_env_line_exist](reference/package_env_manager.check_env_line_exist.html)
- [package_env_manager.load_dependencies](reference/package_env_manager.load_dependencies.html)
- [py_collect_gene_entrezid.py_gene_from_hipathia](reference/py_collect_gene_entrezid.py_gene_from_hipathia.html)
- [py_collect_gene_entrezid.py_gene_id_entrez_converter](reference/py_collect_gene_entrezid.py_gene_id_entrez_converter.html)
- [run_dependency.main](reference/run_dependency.main.html)
- [run_dependency.run_dependency_installer](reference/run_dependency.run_dependency_installer.html)
- [run_dependency.setup_project_env](reference/run_dependency.setup_project_env.html)
- [spn_config.setup_project](reference/spn_config.setup_project.html)

#### Constants
> Module-level constants and data

- [spn_config.DATA_SPN_HELPER_DIR](reference/spn_config.DATA_SPN_HELPER_DIR.html)
- [spn_config.DISEASE_KEYWORD](reference/spn_config.DISEASE_KEYWORD.html)
- [spn_config.DISEASE_LIST](reference/spn_config.DISEASE_LIST.html)
- [spn_config.GA_DICT](reference/spn_config.GA_DICT.html)
- [spn_config.PROCESSED_DIR](reference/spn_config.PROCESSED_DIR.html)
- [spn_config.RAW_DIR](reference/spn_config.RAW_DIR.html)