Index

A

add_cytoscape_html_report() (visual.ReportGenerator.ReportGenerator method)

add_section() (visual.ReportGenerator.ReportGenerator method) add_section_from_file() (visual.ReportGenerator.ReportGenerator method)

B

build_edge_metrics_df() (graph.PPINetwork.PPINetwork method)

build_node_metrics_df() (graph.PPINetwork.PPINetwork method)

C

compute_all_edge_metrics() (graph.PPINetwork.PPINetwork method) compute_all_global_metrics() (graph.PPINetwork.PPINetwork method) compute_all_metrics() (graph.PPINetwork.PPINetwork method) compute_all_node_metrics() (graph.PPINetwork.PPINetwork method) compute_average_clustering() (graph.PPINetwork.PPINetwork method) compute_average_neighbor_degree() (graph.PPINetwork.PPINetwork method) compute_average_shortest_path_length() (graph.PPINetwork.PPINetwork method) compute_betweenness_centrality() (graph.PPINetwork.PPINetwork method) compute_bridging_centrality() (graph.PPINetwork.PPINetwork method) compute_closeness_centrality() (graph.PPINetwork.PPINetwork method) compute_clustering_coefficient() (graph.PPINetwork.PPINetwork method) compute_communities() (graph.PPINetwork.PPINetwork method) compute_community_roles() (graph.PPINetwork.PPINetwork method) compute_connected_components() (graph.PPINetwork.PPINetwork method) compute_core_number() (graph.PPINetwork.PPINetwork method) compute_degree() (graph.PPINetwork.PPINetwork method) compute_degree_centrality() (graph.PPINetwork.PPINetwork method) compute_density() (graph.PPINetwork.PPINetwork method)

compute_diameter() (graph.PPINetwork.PPINetwork method) compute_edge_betweenness_centrality() (graph.PPINetwork.PPINetwork method) compute_eigenvector_centrality() (graph.PPINetwork.PPINetwork method) compute_global_efficiency() (graph.PPINetwork.PPINetwork method) compute_harmonic_centrality() (graph.PPINetwork.PPINetwork method) compute_is_connected() (graph.PPINetwork.PPINetwork method) compute_katz_centrality() (graph.PPINetwork.PPINetwork method) compute_largest_component_size() (graph.PPINetwork.PPINetwork method) compute_node_removal_impact() (graph.PPINetwork.PPINetwork method) compute_number_connected_components() (graph.PPINetwork.PPINetwork method) compute_number_of_edges() (graph.PPINetwork.PPINetwork method) compute_number_of_nodes() (graph.PPINetwork.PPINetwork method) compute_pagerank() (graph.PPINetwork.PPINetwork method) compute_transitivity() (graph.PPINetwork.PPINetwork method) compute_weighted_degree() (graph.PPINetwork.PPINetwork method) create_barplot_encoded_image() (in module visual.plots_macros) create_graph_degree_distribution_encoded_image() (in module visual.plots_macros) create_scatter_plot_encoded_image() (in module visual.plots_macros)

E

edge_metrics_df (graph.PPINetwork.PPINetwork attribute)

export_for_cytoscape() (graph.PPINetwork.PPINetwork method)

G

G (graph.PPINetwork.PPINetwork attribute) generate_report_file() (visual.ReportGenerator.ReportGenerator method) get_consensus_hub_proteins() (graph.PPINetwork.PPINetwork method) get_data() (graph.Loader.Loader method) get_edges_metric_value() (graph.PPINetwork.PPINetwork method) get_hub_proteins() (graph.PPINetwork.PPINetwork method) get_nodes_metric_value() (graph.PPINetwork.PPINetwork method) get_nodes_preferred_names() (graph.PPINetwork.PPINetwork method)

get_numeric_edge_attrs() (graph.PPINetwork.PPINetwork method) get_numeric_node_attrs() (graph.PPINetwork.PPINetwork method) graph.Loader module graph.PPINetwork module graph_metrics (graph.PPINetwork.PPINetwork attribute) gsea_results_df (graph.PPINetwork.PPINetwork attribute)

H

html_template (visual.ReportGenerator.ReportGenerator attribute)

L

Loader (class in graph.Loader)

M

module graph.Loader graph.PPINetwork visual.plots_macros visual.ReportGenerator

N

networkx_to_cytoscape_elements() (graph.PPINetwork.PPINetwork method)

node_metrics_df (graph.PPINetwork.PPINetwork attribute)

P

plot_gsea_dotplot() (graph.PPINetwork.PPINetwork method)

PPINetwork (class in graph.PPINetwork) prepare_string_weights() (graph.PPINetwork.PPINetwork method)

R

ranked_genes_df (graph.PPINetwork.PPINetwork attribute) ReportGenerator (class in visual.ReportGenerator)

retrieve_data() (graph.Loader.Loader method) run_gsea() (graph.PPINetwork.PPINetwork method)

S

score_attr (graph.PPINetwork.PPINetwork attribute)

standardize_data_format() (graph.Loader.Loader method)

V

visual.plots_macros module

visual.ReportGenerator module