GeneWalk documentation

• GeneWalk modules reference
  • Process gene lists and map between ID types (genewalk.gene_lists)
    • map_ensembl_ids()
    • map_entrez_human()
    • map_entrez_mouse()
    • map_hgnc_ids()
    • map_hgnc_symbols()
    • map_mgi_ids()
    • map_rgd_ids()
    • read_gene_list()
  • Networkx MultiGraph assembler (genewalk.nx_mg_assembler)
    • IndraNxMgAssembler
    • NxMgAssembler
    • PcNxMgAssembler
    • UserNxMgAssembler
    • load_network()
  • Run DeepWalk on a GeneWalk graph (genewalk.deepwalk)
    • DeepWalk
    • run_single_walk()
    • run_walks()
    • run_walks_for_node()
  • Calculate null distributions (genewalk.null_distributions)
    • get_null_distributions()
    • get_rand_graph()
  • Get relevant INDRA Statements (genewalk.get_indra_stmts)
    • download_statements()
    • dump_pickle()
    • filter_to_genes()
    • get_famplex_links()
    • get_famplex_terms()
    • load_genes()
    • load_indra_df()
    • load_mouse_genes()
  • Perform statistics and output results (genewalk.perform_statistics)
    • GeneWalk
  • Plotting results (genewalk.plot)
    • GW_Plotter
  • Manage resource files (genewalk.resources)
    • ResourceManager

Indices and tables

• Index

• Module Index

• Search Page