PICASO.load_utils

Functions

download_and_unzip(download_url_link, dir_path, ...[, ...])
load_go(kg, data_dir[, source, interaction_harmonize])
load_uniprot_location(kg, data_dir[, source])
load_omnipath(kg, data_dir[, source])
load_STRING(kg, data_dir[, mart_file, source, ...])
load_opentargets(kg, data_dir[, source, ...])
load_reactome(kg, data_dir[, source])
load_npinter(kg, data_dir[, source])
load_kegg(kg, data_dir[, source, hallmark_genesets, ...])
load_human_transcription_factors(kg, data_dir[, source])

Module Contents

PICASO.load_utils.download_and_unzip(download_url_link, dir_path, zipped_filename, destination_dir_name, unzip=True, force_zip=False, force_gz=False)

PICASO.load_utils.load_go(kg: networkx.DiGraph, data_dir, source='GeneOntology', interaction_harmonize={'NOT': 'relevant_in', 'acts_upstream_of': 'relevant_in', 'acts_upstream_of_negative_effect': 'relevant_in', 'acts_upstream_of_or_within': 'relevant_in', 'acts_upstream_of_or_within_negative_effect': 'relevant_in', 'acts_upstream_of_or_within_positive_effect': 'relevant_in', 'acts_upstream_of_positive_effect': 'relevant_in', 'colocalizes_with': 'relevant_in', 'contributes_to': 'activates', 'enables': 'activates', 'involved_in': 'relevant_in', 'is_active_in': 'activates', 'located_in': 'relevant_in', 'part_of': 'relevant_in'})

PICASO.load_utils.load_uniprot_location(kg: networkx.DiGraph, data_dir, source='uniprot_celloc')

PICASO.load_utils.load_omnipath(kg: networkx.DiGraph, data_dir, source='omnipath')

PICASO.load_utils.load_STRING(kg: networkx.DiGraph, data_dir, mart_file='oct2014_mart_export.txt', source='STRING', use_evidences=['fusion', 'coexpression', 'experiments', 'database', 'textmining'])

PICASO.load_utils.load_opentargets(kg: networkx.DiGraph, data_dir, source='opentargets', min_disease_association_score=0.8)

PICASO.load_utils.load_reactome(kg: networkx.DiGraph, data_dir, source='reactome')

PICASO.load_utils.load_npinter(kg: networkx.DiGraph, data_dir, source='npinter5')

PICASO.load_utils.load_kegg(kg: networkx.DiGraph, data_dir, source='kegg', hallmark_genesets='kegg_gmts/human/h.all.v2023.2.Hs.symbols.gmt', curated_genesets='kegg_gmts/human/c2.all.v2023.2.Hs.symbols.gmt', load_reactome=False, load_wp=True)

PICASO.load_utils.load_human_transcription_factors(kg: networkx.DiGraph, data_dir, source='human_transcription_factors')