peach.pp.load_pathway_networks

peach.pp.load_pathway_networks(sources=['c5_bp'], *, organism='human', geneset_repo='msigdb', verbose=True, **kwargs)

Load pathway networks from MSigDB or OmniPath.

Parameters:

• sources (List[str], default: ["c5_bp"]) – Pathway sources to load. MSigDB collections: ‘hallmark’, ‘c2_cp’, ‘c2_cgp’, ‘c3_mir’, ‘c5_bp’, ‘c5_cc’, ‘c5_mf’, ‘c8’

• organism (str, default: "human") – Organism to load pathways for: ‘human’ or ‘mouse’

• geneset_repo (str, default: "msigdb") – Repository to use: ‘msigdb’ (recommended) or ‘omnipath’

• verbose (bool, default: True) – Whether to print loading progress

• **kwargs – Additional arguments passed to load_pathway_networks

Returns:

Pathway network with ‘source’, ‘target’, ‘pathway’ columns

Return type:

pd.DataFrame