Index

_

__call__() (PICASO.kgraph.MidpointNormalize method) __missing__() (PICASO.kgraph.DefaultDict method) __repr__() (PICASO.kgraph.KGraph method) _calculate_gs_overlap() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _combined_filter() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _describe_kg() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _filter_edge_score() (PICASO.kgraph.KGraph method) _filter_empty_genesets() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _filter_singletons() (PICASO.kgraph.TwoLevelDifferentialAnalysis method)

_geneset_filter() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _get_diff_comms() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) _get_edge_fold_changes() (PICASO.kgraph.DifferentialKG method) _get_log_foldchange() (PICASO.kgraph.DifferentialKG method) _get_node_fold_changes() (PICASO.kgraph.DifferentialKG method) _get_predecessors() (PICASO.kgraph.KGraph method) _plot_pie() (PICASO.kgraph.KGraph method) _plot_wordcloud() (PICASO.kgraph.AIDescriptor method) _toShortName() (PICASO.kgraph.TwoLevelDifferentialAnalysis method)

A

add_gene_expression() (PICASO.kgraph.KGraph method) adj (PICASO.link_clustering.HLC attribute)

AIDescriptor (class in PICASO.kgraph) annotate_genesets() (PICASO.kgraph.GenesetAnnotator method) available_cellgroups() (PICASO.kgraph.TwoLevelDifferentialAnalysis method)

C

calculate_allegiance() (PICASO.kgraph.CRankExplorer method) calculate_boundary() (PICASO.kgraph.CRankExplorer method) calculate_connectivity() (PICASO.kgraph.CRankExplorer method) calculate_density() (PICASO.kgraph.CRankExplorer method) calculate_diffkg_list() (PICASO.kgraph.DifferentialKG method) calculate_edge_zscores() (PICASO.kgraph.MeanNetworkScorer method) calculate_modules() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) calculate_scores() (PICASO.kgraph.DifferentialCommunityIdentifier method) cellgroupdata (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute) cohend() (PICASO.kgraph.DifferentialCommunityIdentifier class method)

communities (PICASO.kgraph.TwoLevelDifferentialAnalysis property) CommunityTool (class in PICASO.kgraph) compare_modules() (PICASO.kgraph.CommunityTool method) (PICASO.kgraph.NETSIM method) compare_modules_lca() (PICASO.kgraph.NETSIM method) conf_score_accessor (PICASO.kgraph.NETSIM attribute) confidence() (PICASO.kgraph.NETSIM method) copy() (PICASO.kgraph.KGraph method) CRankExplorer (class in PICASO.kgraph) create_overlap_df() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) curr_maxcid (PICASO.link_clustering.HLC attribute)

D

D (PICASO.link_clustering.HLC attribute) Dc() (in module PICASO.link_clustering) DefaultDict (class in PICASO.kgraph) describe_communities() (PICASO.kgraph.KGraph method) describe_module_scrna() (PICASO.kgraph.TwoLevelDifferentialAnalysis method)

describe_modules() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) DifferentialCommunityIdentifier (class in PICASO.kgraph) DifferentialKG (class in PICASO.kgraph) dij() (PICASO.kgraph.NETSIM method) download_and_unzip() (in module PICASO.load_utils) draw_network() (PICASO.kgraph.ModuleCompare method)

E

edge2cid (PICASO.link_clustering.HLC attribute) edges (PICASO.link_clustering.HLC attribute) evaluate_communities() (PICASO.kgraph.CRankExplorer method)

evaluate_community() (PICASO.kgraph.CRankExplorer method) extend_network() (PICASO.kgraph.NetworkExtender method) extend_network_force() (PICASO.kgraph.NetworkExtender method) extend_nodetypes() (PICASO.kgraph.NetworkExtender method)

F

filter_edges() (PICASO.kgraph.KGraph method) filter_nodes() (PICASO.kgraph.KGraph method)

format_epilog() (PICASO.link_clustering.MyParser method) functional_distance_genesets() (PICASO.kgraph.NETSIM method) functional_similarity() (PICASO.kgraph.NETSIM method)

G

GenesetAnnotator (class in PICASO.kgraph) get_annotated_genes() (PICASO.kgraph.NETSIM method) get_communities() (PICASO.kgraph.KGraph method) get_communities_asyn_label_propagation() (PICASO.kgraph.KGraph method) get_communities_connectedcomponent() (PICASO.kgraph.KGraph method) get_communities_ecg() (PICASO.kgraph.KGraph method) get_communities_greedymodularity() (PICASO.kgraph.KGraph method) get_communities_infomap() (PICASO.kgraph.KGraph method) get_communities_link() (PICASO.kgraph.KGraph method) get_communities_markovclustering() (PICASO.kgraph.KGraph method) get_communities_negpos() (PICASO.kgraph.KGraph method) get_community() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) get_community_details() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) get_community_kg() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) get_community_representation() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) get_differential_graph() (PICASO.kgraph.DifferentialKG method) get_edge_attributes() (PICASO.kgraph.KGraph method) get_edge_between_type() (PICASO.kgraph.KGraph method) get_edge_edge_types() (PICASO.kgraph.KGraph method) get_edge_node_types() (PICASO.kgraph.KGraph method) get_edge_scores() (PICASO.kgraph.KGraph method)

get_edge_scores_per_type() (PICASO.kgraph.KGraph method) get_edge_types() (PICASO.kgraph.KGraph method) get_edges_between_ntypes() (PICASO.kgraph.KGraph method) get_edges_to_type() (PICASO.kgraph.KGraph method) get_edges_with_highest_scores() (PICASO.kgraph.KGraph method) get_go_level() (PICASO.kgraph.NETSIM method) get_kg_subgraph() (PICASO.kgraph.KGraph method) get_lca() (PICASO.kgraph.NETSIM method) get_node_attributes() (PICASO.kgraph.KGraph method) get_node_data() (PICASO.kgraph.KGraph method) get_node_degrees() (PICASO.kgraph.KGraph method) get_node_edges() (PICASO.kgraph.KGraph method) get_node_name() (PICASO.kgraph.NETSIM method) get_node_scores() (PICASO.kgraph.KGraph method) get_node_type() (PICASO.kgraph.KGraph method) get_node_types() (PICASO.kgraph.KGraph method) get_nodes() (PICASO.kgraph.KGraph method) get_nodes_with_highest_scores() (PICASO.kgraph.KGraph method) get_nx_subgraph() (PICASO.kgraph.KGraph method) get_path_constrained_annotation() (PICASO.kgraph.NETSIM method) get_relevant_goterms() (PICASO.kgraph.NETSIM method) get_shortest_path() (PICASO.kgraph.NETSIM method)

H

HLC (class in PICASO.link_clustering)

I

identify_differential_communities() (PICASO.kgraph.DifferentialCommunityIdentifier method) induce_kg() (PICASO.kgraph.KGraph method)

initialize_edges() (PICASO.link_clustering.HLC method) is_score_field() (PICASO.kgraph.KGraph method)

K

kg (PICASO.kgraph.KGraph attribute) (PICASO.kgraph.NETSIM attribute)

kg_rev (PICASO.kgraph.NETSIM attribute) KGraph (class in PICASO.kgraph) kgraph_name (PICASO.kgraph.KGraph attribute)

L

lca_similarity() (PICASO.kgraph.NETSIM method) linkage (PICASO.link_clustering.HLC attribute) llm (PICASO.kgraph.AIDescriptor attribute) load_go() (in module PICASO.load_utils) load_human_transcription_factors() (in module PICASO.load_utils) load_kegg() (in module PICASO.load_utils) load_kgraph() (PICASO.kgraph.KGraph method) load_kgraph_base() (PICASO.kgraph.KGraph method)

load_npinter() (in module PICASO.load_utils) load_omnipath() (in module PICASO.load_utils) load_opentargets() (in module PICASO.load_utils) load_reactome() (in module PICASO.load_utils) load_STRING() (in module PICASO.load_utils) load_uniprot_location() (in module PICASO.load_utils) local_dir (PICASO.kgraph.AIDescriptor attribute) logger (PICASO.kgraph.KGraph attribute) (PICASO.kgraph.NetworkScorer attribute)

M

makeProgressBar() (PICASO.kgraph.ModuleCompare class method) max_go_level (PICASO.kgraph.NETSIM attribute) MeanNetworkScorer (class in PICASO.kgraph) merge_comms() (PICASO.link_clustering.HLC method) Mfactor (PICASO.link_clustering.HLC attribute) midpoint (PICASO.kgraph.MidpointNormalize attribute) MidpointNormalize (class in PICASO.kgraph) model_file (PICASO.kgraph.AIDescriptor attribute) model_name (PICASO.kgraph.AIDescriptor attribute)

model_path (PICASO.kgraph.AIDescriptor attribute) module PICASO PICASO.kgraph PICASO.link_clustering PICASO.load_utils module_pca() (PICASO.kgraph.ModuleCompare method) module_similarities_to_df() (PICASO.kgraph.ModuleCompare method) ModuleCompare (class in PICASO.kgraph) MyParser (class in PICASO.link_clustering)

N

name_sep (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute) NETSIM (class in PICASO.kgraph) network_compare_lca() (PICASO.kgraph.ModuleCompare method) network_compare_modules() (PICASO.kgraph.ModuleCompare method)

network_compare_netsim() (PICASO.kgraph.ModuleCompare method) NetworkExtender (class in PICASO.kgraph) NetworkScorer (class in PICASO.kgraph) node_type_overlap() (PICASO.kgraph.KGraph method) node_types() (PICASO.kgraph.KGraph method)

O

orig_cid2edge (PICASO.link_clustering.HLC attribute)

orig_kg (PICASO.kgraph.NETSIM attribute) output_folder_formatter (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute)

P

PICASO module PICASO.kgraph module PICASO.link_clustering module PICASO.load_utils module plot_child_distribution() (PICASO.kgraph.KGraph method) plot_community() (PICASO.kgraph.CommunityTool method) plot_dendrogram() (PICASO.kgraph.ModuleCompare method) plot_edge_attribute_distribution() (PICASO.kgraph.KGraph method) plot_edge_between_types() (PICASO.kgraph.KGraph method) plot_edge_types() (PICASO.kgraph.KGraph method)

plot_graph() (PICASO.kgraph.KGraph method) plot_graph_network() (PICASO.kgraph.KGraph method) plot_module_comparisons() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) plot_module_description() (PICASO.kgraph.TwoLevelDifferentialAnalysis method) plot_node_attribute_distribution() (PICASO.kgraph.KGraph method) plot_node_attribute_histogram() (PICASO.kgraph.KGraph method) plot_node_children() (PICASO.kgraph.KGraph method) plot_node_types() (PICASO.kgraph.KGraph method) plot_score_histogram() (PICASO.kgraph.KGraph method) plot_score_violin() (PICASO.kgraph.KGraph method) plot_scores() (PICASO.kgraph.CRankExplorer method) plot_subgraph_scores() (PICASO.kgraph.KGraph method) precalculated_term_genes (PICASO.kgraph.NETSIM attribute) print_kg_info() (PICASO.kgraph.KGraph method) pseudocount (PICASO.kgraph.DifferentialKG attribute)

Q

query_genelist() (PICASO.kgraph.AIDescriptor method)

query_wordcloud() (PICASO.kgraph.AIDescriptor method)

R

random_state (PICASO.kgraph.KGraph attribute) (PICASO.kgraph.NetworkScorer attribute)

read_edgelist_unweighted() (in module PICASO.link_clustering) read_edgelist_weighted() (in module PICASO.link_clustering) recalc_warning (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute)

S

save_kgraph() (PICASO.kgraph.KGraph method) scatter_community_scores() (PICASO.kgraph.CommunityTool method) score() (PICASO.kgraph.MeanNetworkScorer method) (PICASO.kgraph.NetworkScorer method) score_edges() (PICASO.kgraph.MeanNetworkScorer method) score_nodes_from_edges() (PICASO.kgraph.MeanNetworkScorer method) score_nodes_from_properties() (PICASO.kgraph.MeanNetworkScorer method) score_nodes_hierarchically() (PICASO.kgraph.KGraph method) score_nx() (PICASO.kgraph.MeanNetworkScorer method) score_subgraphs() (PICASO.kgraph.DifferentialCommunityIdentifier method)

score_subgraphs_for_subnet() (PICASO.kgraph.DifferentialCommunityIdentifier method) scoring_gene_gene_expression (PICASO.kgraph.MeanNetworkScorer attribute) scoring_interactions (PICASO.kgraph.MeanNetworkScorer attribute) similarities_unweighted() (in module PICASO.link_clustering) similarities_weighted() (in module PICASO.link_clustering) single_linkage() (PICASO.link_clustering.HLC method) sjoined() (in module PICASO.kgraph) sort_communities() (PICASO.kgraph.CommunityTool method) sorted_zones (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute) subset_kg() (PICASO.kgraph.KGraph method) swap() (in module PICASO.link_clustering)

T

tldict (PICASO.kgraph.TwoLevelDifferentialAnalysis attribute)

to_gene_kgraph() (PICASO.kgraph.KGraph method) TwoLevelDifferentialAnalysis (class in PICASO.kgraph)

U

undirected_x (PICASO.kgraph.NETSIM attribute)

V

visualize_communities() (PICASO.kgraph.CommunityTool method)

W

write_dendro() (in module PICASO.link_clustering)

write_edge2cid() (in module PICASO.link_clustering)