Index

A

A() (in module multi_dendrix) avg_pair_dist_of_gene_set() (in module multi_dendrix.evaluate.network)

avg_pair_dist_ratio() (in module multi_dendrix.evaluate.network) avg_pair_dist_test() (in module multi_dendrix.evaluate.network)

B

batch_multi_dendrix (module) batch_multi_dendrix() (in module multi_dendrix_pipeline)

bipartite_double_edge_swap() (in module multi_dendrix.permute.mutation_data)

C

construct_mutation_graph() (in module multi_dendrix.permute.mutation_data)

count_interactions() (in module multi_dendrix.evaluate.network)

D

direct_interactions_stat() (in module multi_dendrix.evaluate.network) direct_interactions_test (module)

direct_interactions_test() (in module multi_dendrix.evaluate.network) dist() (in module multi_dendrix.evaluate.network)

E

eval_gene_sets_by_dist() (in module multi_dendrix.evaluate.network) eval_gene_sets_by_interactions() (in module multi_dendrix.evaluate.network)

evaluate_collection() (in module multi_dendrix.evaluate.network) extract() (in module multi_dendrix.core_modules)

G

generating_permuted_matrices (module) generating_permuted_networks (module)

graph_to_mutation_data() (in module multi_dendrix.permute.mutation_data)

I

ILP() (in module multi_dendrix)

interact() (in module multi_dendrix.evaluate.network)

K

keep_significant() (in module multi_dendrix.subtypes)

L

load_collection() (in module multi_dendrix.evaluate.network) load_mutation_data() (in module multi_dendrix) load_mutation_data_w_cutoff() (in module multi_dendrix) load_network() (in module multi_dendrix.permute.ppi_network)

load_patient2ty_file() (in module multi_dendrix.subtypes) load_permuted_matrices() (in module multi_dendrix.evaluate.matrix) load_w_prime() (in module multi_dendrix.evaluate.matrix)

M

matrix_permutation_test() (in module multi_dendrix.evaluate.matrix)

N

num_interactions_in_gene_set() (in module multi_dendrix.evaluate.network)

P

permute_mutation_data() (in module multi_dendrix.permute.mutation_data)

permute_network() (in module multi_dendrix.permute.ppi_network)

R

remove_name_annotation() (in module multi_dendrix.evaluate.network) run() (in module batch_multi_dendrix) (in module direct_interactions_test) (in module generating_permuted_matrices) (in module generating_permuted_networks) (in module multi_dendrix_pipeline) (in module subtype_specific_mutations) (in module weight_permutation_test)

run_matrix_permutation_test() (in module multi_dendrix_pipeline) run_network_permutation_test() (in module multi_dendrix_pipeline)

S

subtype_analysis() (in module multi_dendrix.subtypes) subtype_specific_mutations (module)

subtype_specificity() (in module multi_dendrix.subtypes) sum_dist() (in module multi_dendrix.evaluate.network)

T

ty_contingency_table() (in module multi_dendrix.subtypes)

W

W() (in module multi_dendrix) weight_permutation_test (module)

white_and_blacklisting() (in module multi_dendrix)