Index

A

add_agent_node() (genewalk.nx_mg_assembler.IndraNxMgAssembler method) add_fplx_edges() (genewalk.nx_mg_assembler.IndraNxMgAssembler method) add_go_annotations() (genewalk.nx_mg_assembler.NxMgAssembler method)

add_go_ontology() (genewalk.nx_mg_assembler.NxMgAssembler method) add_indra_edges() (genewalk.nx_mg_assembler.IndraNxMgAssembler method) add_network_edges() (genewalk.nx_mg_assembler.UserNxMgAssembler method) add_pc_edges() (genewalk.nx_mg_assembler.PcNxMgAssembler method)

B

barplot_goanno() (genewalk.plot.GW_Plotter method)

D

DeepWalk (class in genewalk.deepwalk)

download_statements() (in module genewalk.get_indra_stmts) dump_pickle() (in module genewalk.get_indra_stmts)

F

filter_to_genes() (in module genewalk.get_indra_stmts)

G

generate_output() (genewalk.perform_statistics.GeneWalk method) generate_plots() (genewalk.plot.GW_Plotter method) GeneWalk (class in genewalk.perform_statistics) genewalk.deepwalk module genewalk.gene_lists module genewalk.get_indra_stmts module genewalk.null_distributions module genewalk.nx_mg_assembler module genewalk.perform_statistics module genewalk.plot module

genewalk.resources module get_famplex_links() (in module genewalk.get_indra_stmts) get_famplex_terms() (in module genewalk.get_indra_stmts) get_gene_attribs() (genewalk.perform_statistics.GeneWalk method) get_go_attribs() (genewalk.perform_statistics.GeneWalk method) get_null_distributions() (in module genewalk.null_distributions) get_rand_graph() (in module genewalk.null_distributions) get_walks() (genewalk.deepwalk.DeepWalk method) global_fdr() (genewalk.perform_statistics.GeneWalk method) graph (genewalk.nx_mg_assembler.IndraNxMgAssembler attribute) (genewalk.nx_mg_assembler.NxMgAssembler attribute) (genewalk.nx_mg_assembler.PcNxMgAssembler attribute) (genewalk.nx_mg_assembler.UserNxMgAssembler attribute) GW_Plotter (class in genewalk.plot)

I

IndraNxMgAssembler (class in genewalk.nx_mg_assembler)

L

load_genes() (in module genewalk.get_indra_stmts) load_indra_df() (in module genewalk.get_indra_stmts)

load_mouse_genes() (in module genewalk.get_indra_stmts) load_network() (in module genewalk.nx_mg_assembler)

M

make_html() (genewalk.plot.GW_Plotter method) map_ensembl_ids() (in module genewalk.gene_lists) map_entrez_human() (in module genewalk.gene_lists) map_entrez_mouse() (in module genewalk.gene_lists) map_hgnc_ids() (in module genewalk.gene_lists) map_hgnc_symbols() (in module genewalk.gene_lists) map_mgi_ids() (in module genewalk.gene_lists) map_rgd_ids() (in module genewalk.gene_lists)

module genewalk.deepwalk genewalk.gene_lists genewalk.get_indra_stmts genewalk.null_distributions genewalk.nx_mg_assembler genewalk.perform_statistics genewalk.plot genewalk.resources

N

node2edges() (genewalk.nx_mg_assembler.NxMgAssembler method)

node2stmts() (genewalk.nx_mg_assembler.IndraNxMgAssembler method) NxMgAssembler (class in genewalk.nx_mg_assembler)

P

PcNxMgAssembler (class in genewalk.nx_mg_assembler)

psim() (genewalk.perform_statistics.GeneWalk method)

R

read_gene_list() (in module genewalk.gene_lists) ResourceManager (class in genewalk.resources)

run_single_walk() (in module genewalk.deepwalk) run_walks() (in module genewalk.deepwalk) run_walks_for_node() (in module genewalk.deepwalk)

S

save_graph() (genewalk.nx_mg_assembler.NxMgAssembler method)

scatterplot_moonlighters() (genewalk.plot.GW_Plotter method) scatterplot_regulators() (genewalk.plot.GW_Plotter method)

U

UserNxMgAssembler (class in genewalk.nx_mg_assembler)

W

walks (genewalk.deepwalk.DeepWalk attribute)

word2vec() (genewalk.deepwalk.DeepWalk method)