API

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• PICASO
  • Submodules
    • PICASO.kgraph
      • Classes
      • Functions
      • Module Contents
        • MidpointNormalize
          • MidpointNormalize.midpoint
          • MidpointNormalize.__call__()
        • sjoined()
        • KGraph
          • KGraph.kg
          • KGraph.random_state
          • KGraph.kgraph_name
          • KGraph.logger
          • KGraph.is_score_field()
          • KGraph.get_node_attributes()
          • KGraph.get_edge_attributes()
          • KGraph.__repr__()
          • KGraph.copy()
          • KGraph.print_kg_info()
          • KGraph.load_kgraph_base()
          • KGraph.load_kgraph()
          • KGraph.save_kgraph()
          • KGraph.get_node_data()
          • KGraph.get_node_edges()
          • KGraph.get_nodes()
          • KGraph.get_nodes_with_highest_scores()
          • KGraph.get_edges_with_highest_scores()
          • KGraph.node_types()
          • KGraph.get_node_types()
          • KGraph.plot_node_types()
          • KGraph.plot_node_children()
          • KGraph.plot_child_distribution()
          • KGraph.plot_edge_types()
          • KGraph.plot_edge_between_types()
          • KGraph._plot_pie()
          • KGraph.get_edge_types()
          • KGraph.get_edge_node_types()
          • KGraph.get_edge_edge_types()
          • KGraph.get_edge_between_type()
          • KGraph.add_gene_expression()
          • KGraph.get_node_type()
          • KGraph.get_edges_to_type()
          • KGraph.get_edges_between_ntypes()
          • KGraph._get_predecessors()
          • KGraph.score_nodes_hierarchically()
          • KGraph.node_type_overlap()
          • KGraph.get_node_scores()
          • KGraph.get_edge_scores()
          • KGraph.get_edge_scores_per_type()
          • KGraph.plot_score_histogram()
          • KGraph.plot_edge_attribute_distribution()
          • KGraph.plot_node_attribute_distribution()
          • KGraph.plot_node_attribute_histogram()
          • KGraph.plot_score_violin()
          • KGraph.plot_subgraph_scores()
          • KGraph.filter_nodes()
          • KGraph.filter_edges()
          • KGraph.subset_kg()
          • KGraph.induce_kg()
          • KGraph.to_gene_kgraph()
          • KGraph._filter_edge_score()
          • KGraph.get_communities_connectedcomponent()
          • KGraph.get_communities_greedymodularity()
          • KGraph.get_communities_asyn_label_propagation()
          • KGraph.get_communities()
          • KGraph.get_communities_ecg()
          • KGraph.get_communities_negpos()
          • KGraph.get_communities_infomap()
          • KGraph.get_communities_markovclustering()
          • KGraph.get_communities_link()
          • KGraph.describe_communities()
          • KGraph.get_kg_subgraph()
          • KGraph.plot_graph_network()
          • KGraph.get_nx_subgraph()
          • KGraph.plot_graph()
          • KGraph.get_node_degrees()
        • NetworkScorer
          • NetworkScorer.random_state
          • NetworkScorer.logger
          • NetworkScorer.score()
        • MeanNetworkScorer
          • MeanNetworkScorer.scoring_gene_gene_expression
          • MeanNetworkScorer.scoring_interactions
          • MeanNetworkScorer.score_edges()
          • MeanNetworkScorer.score_nodes_from_properties()
          • MeanNetworkScorer.score_nodes_from_edges()
          • MeanNetworkScorer.score_nx()
          • MeanNetworkScorer.score()
          • MeanNetworkScorer.calculate_edge_zscores()
        • NetworkExtender
          • NetworkExtender.extend_network()
          • NetworkExtender.extend_network_force()
          • NetworkExtender.extend_nodetypes()
        • CommunityTool
          • CommunityTool.scatter_community_scores()
          • CommunityTool.visualize_communities()
          • CommunityTool.sort_communities()
          • CommunityTool.plot_community()
          • CommunityTool.compare_modules()
        • DifferentialCommunityIdentifier
          • DifferentialCommunityIdentifier.cohend()
          • DifferentialCommunityIdentifier.calculate_scores()
          • DifferentialCommunityIdentifier.identify_differential_communities()
          • DifferentialCommunityIdentifier.score_subgraphs_for_subnet()
          • DifferentialCommunityIdentifier.score_subgraphs()
        • GenesetAnnotator
          • GenesetAnnotator.annotate_genesets()
        • DifferentialKG
          • DifferentialKG.pseudocount
          • DifferentialKG._get_edge_fold_changes()
          • DifferentialKG._get_log_foldchange()
          • DifferentialKG._get_node_fold_changes()
          • DifferentialKG.get_differential_graph()
          • DifferentialKG.calculate_diffkg_list()
        • NETSIM
          • NETSIM.kg
          • NETSIM.orig_kg
          • NETSIM.conf_score_accessor
          • NETSIM.kg_rev
          • NETSIM.undirected_x
          • NETSIM.max_go_level
          • NETSIM.precalculated_term_genes
          • NETSIM.get_annotated_genes()
          • NETSIM.confidence()
          • NETSIM.dij()
          • NETSIM.functional_distance_genesets()
          • NETSIM.get_lca()
          • NETSIM.get_shortest_path()
          • NETSIM.get_path_constrained_annotation()
          • NETSIM.get_node_name()
          • NETSIM.functional_similarity()
          • NETSIM.get_go_level()
          • NETSIM.lca_similarity()
          • NETSIM.get_relevant_goterms()
          • NETSIM.compare_modules_lca()
          • NETSIM.compare_modules()
        • ModuleCompare
          • ModuleCompare.makeProgressBar()
          • ModuleCompare.draw_network()
          • ModuleCompare.module_similarities_to_df()
          • ModuleCompare.network_compare_modules()
          • ModuleCompare.network_compare_lca()
          • ModuleCompare.network_compare_netsim()
          • ModuleCompare.module_pca()
          • ModuleCompare.plot_dendrogram()
        • CRankExplorer
          • CRankExplorer.calculate_connectivity()
          • CRankExplorer.calculate_density()
          • CRankExplorer.calculate_boundary()
          • CRankExplorer.calculate_allegiance()
          • CRankExplorer.evaluate_community()
          • CRankExplorer.evaluate_communities()
          • CRankExplorer.plot_scores()
        • DefaultDict
          • DefaultDict.__missing__()
        • TwoLevelDifferentialAnalysis
          • TwoLevelDifferentialAnalysis.tldict
          • TwoLevelDifferentialAnalysis.sorted_zones
          • TwoLevelDifferentialAnalysis.name_sep
          • TwoLevelDifferentialAnalysis.cellgroupdata
          • TwoLevelDifferentialAnalysis.output_folder_formatter
          • TwoLevelDifferentialAnalysis.recalc_warning
          • TwoLevelDifferentialAnalysis.calculate_modules()
          • TwoLevelDifferentialAnalysis._get_diff_comms()
          • TwoLevelDifferentialAnalysis.plot_module_comparisons()
          • TwoLevelDifferentialAnalysis._geneset_filter()
          • TwoLevelDifferentialAnalysis._filter_empty_genesets()
          • TwoLevelDifferentialAnalysis._filter_singletons()
          • TwoLevelDifferentialAnalysis._combined_filter()
          • TwoLevelDifferentialAnalysis.communities
          • TwoLevelDifferentialAnalysis.get_community()
          • TwoLevelDifferentialAnalysis.get_community_details()
          • TwoLevelDifferentialAnalysis.get_community_kg()
          • TwoLevelDifferentialAnalysis.get_community_representation()
          • TwoLevelDifferentialAnalysis.plot_module_description()
          • TwoLevelDifferentialAnalysis._describe_kg()
          • TwoLevelDifferentialAnalysis.describe_modules()
          • TwoLevelDifferentialAnalysis.create_overlap_df()
          • TwoLevelDifferentialAnalysis._calculate_gs_overlap()
          • TwoLevelDifferentialAnalysis._toShortName()
          • TwoLevelDifferentialAnalysis.describe_module_scrna()
          • TwoLevelDifferentialAnalysis.available_cellgroups()
        • AIDescriptor
          • AIDescriptor.model_name
          • AIDescriptor.model_file
          • AIDescriptor.local_dir
          • AIDescriptor.model_path
          • AIDescriptor.llm
          • AIDescriptor.query_genelist()
          • AIDescriptor._plot_wordcloud()
          • AIDescriptor.query_wordcloud()
    • PICASO.link_clustering
      • Classes
      • Functions
      • Module Contents
        • swap()
        • Dc()
        • HLC
          • HLC.adj
          • HLC.edges
          • HLC.Mfactor
          • HLC.edge2cid
          • HLC.orig_cid2edge
          • HLC.curr_maxcid
          • HLC.linkage
          • HLC.D
          • HLC.initialize_edges()
          • HLC.merge_comms()
          • HLC.single_linkage()
        • similarities_unweighted()
        • similarities_weighted()
        • read_edgelist_unweighted()
        • read_edgelist_weighted()
        • write_edge2cid()
        • write_dendro()
        • MyParser
          • MyParser.format_epilog()
    • PICASO.load_utils
      • Functions
      • Module Contents
        • download_and_unzip()
        • load_go()
        • load_uniprot_location()
        • load_omnipath()
        • load_STRING()
        • load_opentargets()
        • load_reactome()
        • load_npinter()
        • load_kegg()
        • load_human_transcription_factors()