Index

A

annotate_local_neighborhood() (EndotypY.endotyper.Endotyper method)

C

calculate_top_genes() (in module EndotypY.expansion) compute_feature_matrix() (in module EndotypY.kl_clustering)

convert_entrez_to_symbols() (in module EndotypY.utils) convert_gs_lib_to_dict() (in module EndotypY.expansion) convert_symbols_to_entrez() (in module EndotypY.utils)

D

define_kl_endotypes() (EndotypY.endotyper.Endotyper method)

define_local_neighborhood() (EndotypY.endotyper.Endotyper method) download_enrichr_library() (in module EndotypY.utils)

E

Endotyper (class in EndotypY.endotyper) EndotypY module EndotypY.endotyper module EndotypY.expansion module EndotypY.import_export module EndotypY.kl_clustering module EndotypY.metagraph_visualization module

EndotypY.prepare_rwr module EndotypY.rwr module EndotypY.seed_clusters module EndotypY.utils module EndotypY.visualization module explore_seed_clusters() (EndotypY.endotyper.Endotyper method) extract_connected_module() (in module EndotypY.rwr) extract_disease_module() (EndotypY.endotyper.Endotyper method)

G

get_gene_and_neighborhood_enrichment_terms() (in module EndotypY.expansion)

get_GSEA_significant_terms() (in module EndotypY.expansion) get_module_neighborhood_terms_dict() (in module EndotypY.expansion)

I

import_network() (EndotypY.endotyper.Endotyper method)

import_seeds() (EndotypY.endotyper.Endotyper method)

K

kl_clustering_endotypes() (in module EndotypY.kl_clustering)

L

load_seed_set_from_file() (in module EndotypY.import_export)

M

make_p0() (in module EndotypY.rwr) module EndotypY EndotypY.endotyper EndotypY.expansion EndotypY.import_export EndotypY.kl_clustering EndotypY.metagraph_visualization EndotypY.prepare_rwr EndotypY.rwr EndotypY.seed_clusters EndotypY.utils EndotypY.visualization

P

plot_endotype() (in module EndotypY.visualization) plot_endotype_grid() (EndotypY.endotyper.Endotyper method) (in module EndotypY.visualization) plot_endotypes() (EndotypY.endotyper.Endotyper method) plot_endotypes_metagraph() (EndotypY.endotyper.Endotyper method) (in module EndotypY.metagraph_visualization)

plot_multiple_endotypes() (in module EndotypY.visualization) prep_rwr() (in module EndotypY.prepare_rwr) prepare_rwr() (EndotypY.endotyper.Endotyper method) process_gene() (in module EndotypY.expansion)

R

read_network_from_file() (in module EndotypY.import_export) run_seed_clustering() (in module EndotypY.seed_clusters)

rwr() (in module EndotypY.rwr) rwr_from_individual_genes() (in module EndotypY.rwr)