# API Reference


## Classes


Main classes provided by the package


[path_manager.ProjectPaths](path_manager.ProjectPaths.md#sigpathmatrix.path_manager.ProjectPaths)  
Manage project paths dynamically


## Functions


Utility functions


[collect_bio_layer.collect_hipathia_pathway()](collect_bio_layer.collect_hipathia_pathway.md#sigpathmatrix.collect_bio_layer.collect_hipathia_pathway)  
Collecting HiPathia pathway information for the given species and export into given data folder.

[collect_bio_layer.create_pbk_matrix_hipathia_signaling()](collect_bio_layer.create_pbk_matrix_hipathia_signaling.md#sigpathmatrix.collect_bio_layer.create_pbk_matrix_hipathia_signaling)  
Exporting pathway and circuit dataset. The exported data gene vs pathway/circuit. It shows the connection details of each pathway-gene and circuit-gene pairs.

[collect_bio_layer.remove_disease_pathways()](collect_bio_layer.remove_disease_pathways.md#sigpathmatrix.collect_bio_layer.remove_disease_pathways)  
Removing disease-associated pathways from collected data. The data, by default, is collecting from HiPathia package. The raw data (input_pathway) is a list of pathway name and ID pairs.

[default_pbk_hipathia.convert_custom_list_into_list()](default_pbk_hipathia.convert_custom_list_into_list.md#sigpathmatrix.default_pbk_hipathia.convert_custom_list_into_list)  

[default_pbk_hipathia.main()](default_pbk_hipathia.main.md#sigpathmatrix.default_pbk_hipathia.main)  
The entry point of collecting and exporting signaling pathways/circuits matrix

[default_pbk_hipathia.process_default_pbk()](default_pbk_hipathia.process_default_pbk.md#sigpathmatrix.default_pbk_hipathia.process_default_pbk)  
The main script that collects and export the signaling pathway/circut matrix.

[package_env_manager.check_env_line_exist()](package_env_manager.check_env_line_exist.md#sigpathmatrix.package_env_manager.check_env_line_exist)  
Checking the PYTHON and R environment information in .env file

[package_env_manager.load_dependencies()](package_env_manager.load_dependencies.md#sigpathmatrix.package_env_manager.load_dependencies)  
Locate and parse the dependencies.yml file which contains

[py_collect_gene_entrezid.py_gene_from_hipathia()](py_collect_gene_entrezid.py_gene_from_hipathia.md#sigpathmatrix.py_collect_gene_entrezid.py_gene_from_hipathia)  
Calling helper R-script to collect gene from HiPathia package.

[py_collect_gene_entrezid.py_gene_id_entrez_converter()](py_collect_gene_entrezid.py_gene_id_entrez_converter.md#sigpathmatrix.py_collect_gene_entrezid.py_gene_id_entrez_converter)  
Calling helper R-script to collect gene from HiPathia package.

[run_dependency.main()](run_dependency.main.md#sigpathmatrix.run_dependency.main)  
The entry points of downloading dependency list

[run_dependency.run_dependency_installer()](run_dependency.run_dependency_installer.md#sigpathmatrix.run_dependency.run_dependency_installer)  
Execution the installation of the essential package which are

[run_dependency.setup_project_env()](run_dependency.setup_project_env.md#sigpathmatrix.run_dependency.setup_project_env)  
Generate .env file and defining the PYTHON and R environment.

[spn_config.setup_project()](spn_config.setup_project.md#sigpathmatrix.spn_config.setup_project)  
Initialize project directories


## Constants


Module-level constants and data


[spn_config.DATA_SPN_HELPER_DIR](spn_config.DATA_SPN_HELPER_DIR.md#sigpathmatrix.spn_config.DATA_SPN_HELPER_DIR)  

[spn_config.DISEASE_KEYWORD](spn_config.DISEASE_KEYWORD.md#sigpathmatrix.spn_config.DISEASE_KEYWORD)  

[spn_config.DISEASE_LIST](spn_config.DISEASE_LIST.md#sigpathmatrix.spn_config.DISEASE_LIST)  

[spn_config.GA_DICT](spn_config.GA_DICT.md#sigpathmatrix.spn_config.GA_DICT)  

[spn_config.PROCESSED_DIR](spn_config.PROCESSED_DIR.md#sigpathmatrix.spn_config.PROCESSED_DIR)  

[spn_config.RAW_DIR](spn_config.RAW_DIR.md#sigpathmatrix.spn_config.RAW_DIR)