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
    • IndraNxMgAssembler.graph
    • IndraNxMgAssembler.add_agent_node()
    • IndraNxMgAssembler.add_fplx_edges()
    • IndraNxMgAssembler.add_indra_edges()
    • IndraNxMgAssembler.node2stmts()
  • NxMgAssembler
    • NxMgAssembler.graph
    • NxMgAssembler.add_go_annotations()
    • NxMgAssembler.add_go_ontology()
    • NxMgAssembler.node2edges()
    • NxMgAssembler.save_graph()
  • PcNxMgAssembler
    • PcNxMgAssembler.graph
    • PcNxMgAssembler.add_pc_edges()
  • UserNxMgAssembler
    • UserNxMgAssembler.graph
    • UserNxMgAssembler.add_network_edges()
  • load_network()
• Run DeepWalk on a GeneWalk graph (genewalk.deepwalk)
  • DeepWalk
    • DeepWalk.walks
    • DeepWalk.get_walks()
    • DeepWalk.word2vec()
  • 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
    • GeneWalk.generate_output()
    • GeneWalk.get_gene_attribs()
    • GeneWalk.get_go_attribs()
    • GeneWalk.global_fdr()
    • GeneWalk.psim()
• Plotting results (genewalk.plot)
  • GW_Plotter
    • GW_Plotter.barplot_goanno()
    • GW_Plotter.generate_plots()
    • GW_Plotter.make_html()
    • GW_Plotter.scatterplot_moonlighters()
    • GW_Plotter.scatterplot_regulators()
• Manage resource files (genewalk.resources)
  • ResourceManager