Index

A

ActiveForward (metworkpy.imat.imat_iter.ReactionActivity attribute) ActiveReverse (metworkpy.imat.imat_iter.ReactionActivity attribute) add_imat_constraints() (in module metworkpy.imat.imat_functions) add_imat_constraints_() (in module metworkpy.imat.imat_functions) add_imat_objective() (in module metworkpy.imat.imat_functions)

add_imat_objective_() (in module metworkpy.imat.imat_functions) add_metabolite_absorb_reaction_() (in module metworkpy.metabolites.metabolite_network) add_metabolite_objective_() (in module metworkpy.metabolites.metabolite_network) add_metchange_objective_constraint_() (in module metworkpy.metabolites.metchange_functions) auc_roc (metworkpy.utils.statistics.MannWhitneyUResult attribute)

B

betweenness_centrality_bipartite_subset() (in module metworkpy.network.centrality)

betweenness_centrality_subset() (in module metworkpy.network.centrality) bipartite_project() (in module metworkpy.network.projection)

C

calculate_divergence_grouped() (in module metworkpy.divergence.group_divergence) calculate_reaction_neighborhood_divergence() (in module metworkpy.divergence.group_divergence) closeness_centrality_subset() (in module metworkpy.network.centrality) compute_imat_objective() (in module metworkpy.imat.imat_functions) corner_sampling() (in module metworkpy.sampling.corners) count_to_cpm() (in module metworkpy.utils.expression_utils) count_to_fpkm() (in module metworkpy.utils.expression_utils) count_to_rpkm() (in module metworkpy.utils.expression_utils) count_to_tpm() (in module metworkpy.utils.expression_utils)

create_adjacency_matrix() (in module metworkpy.network.network_construction) create_gene_network() (in module metworkpy.network.network_construction) create_group_distance_adjacency_matrix() (in module metworkpy.network.network_construction) create_group_distance_network() (in module metworkpy.network.network_construction) create_group_neighborhood_network() (in module metworkpy.network.network_construction) create_grouped_mi_network() (in module metworkpy.information.mutual_information_network) create_metabolic_network() (in module metworkpy.network.network_construction) create_metabolite_network() (in module metworkpy.network.network_construction) create_mutual_information_network() (in module metworkpy.network.network_construction) create_reaction_network() (in module metworkpy.network.network_construction)

E

eliminate_maintenance_requirements_() (in module metworkpy.metabolites.metabolite_network) eval_gpr() (in module metworkpy.gpr.gpr_functions)

expr_to_imat_gene_weights() (in module metworkpy.utils.expression_utils) expr_to_metchange_gene_weights() (in module metworkpy.utils.expression_utils) extended_mannwhitneyu_test() (in module metworkpy.utils.statistics)

F

fast_ess_genes() (in module metworkpy.synleth.fastess) fast_ess_rxn() (in module metworkpy.synleth.fastess) find_connected_components() (in module metworkpy.utils.connected_components) find_degree() (in module metworkpy.utils.connected_components) find_dense_clusters() (in module metworkpy.network.density) find_metabolite_consuming_network_genes() (in module metworkpy.metabolites.metabolite_network) find_metabolite_consuming_network_reactions() (in module metworkpy.metabolites.metabolite_network) find_metabolite_network_enrichment() (in module metworkpy.metabolites.metabolite_network) find_metabolite_synthesis_network_genes() (in module metworkpy.metabolites.metabolite_network) find_metabolite_synthesis_network_reactions() (in module metworkpy.metabolites.metabolite_network)

find_neighbors() (in module metworkpy.utils.connected_components) find_representative_nodes() (in module metworkpy.utils.connected_components) find_synthetic_lethal_genes() (in module metworkpy.synleth.fastsl) find_variable_components() (in module metworkpy.network.components) fisher_enrichment() (in module metworkpy.utils.statistics) flux_to_binary() (in module metworkpy.imat.imat_functions) fpkm_to_tpm() (in module metworkpy.utils.expression_utils) fuzzy_reaction_intersection() (in module metworkpy.network.fuzzy) fuzzy_reaction_set() (in module metworkpy.network.fuzzy) FuzzyMembershipFunction (class in metworkpy.network.fuzzy) fva_model() (in module metworkpy.imat.model_creation)

G

gene_target_density() (in module metworkpy.network.density) gene_target_enrichment() (in module metworkpy.network.density) gene_to_reaction_ids() (in module metworkpy.utils.translate) gene_to_reaction_list() (in module metworkpy.utils.translate) gene_to_rxn_weights() (in module metworkpy.gpr.gpr_functions) generate_model() (in module metworkpy.imat.model_creation) get_gene_to_reaction_translation_dict() (in module metworkpy.utils.translate) get_graph_neighborhood() (in module metworkpy.network.neighborhoods)

get_graph_neighborhood_group() (in module metworkpy.network.neighborhoods) get_reaction_to_gene_translation_dict() (in module metworkpy.utils.translate) get_top_metabolite_pairs() (in module metworkpy.network.network_construction) get_top_metabolites() (in module metworkpy.network.network_construction) geweke() (in module metworkpy.sampling.diagnostics) graph_gene_neighborhood_iter() (in module metworkpy.network.neighborhoods) graph_gene_neighborhoods() (in module metworkpy.network.neighborhoods) graph_neighborhood_iter() (in module metworkpy.network.neighborhoods) graph_neighborhoods() (in module metworkpy.network.neighborhoods)

H

HashableComparable (class in metworkpy.utils.connected_components)

I

imat() (in module metworkpy.imat.imat_functions) imat_constraint_model() (in module metworkpy.imat.model_creation) imat_iter_flux_sample() (in module metworkpy.imat.imat_iter) ImatBinaryVariables (class in metworkpy.imat.imat_iter) ImatIter (class in metworkpy.imat.imat_iter)

ImatIterBase (class in metworkpy.imat.imat_iter) ImatIterBinaryVariables (class in metworkpy.imat.imat_iter) ImatIterModels (class in metworkpy.imat.imat_iter) ImatIterReactionActivities (class in metworkpy.imat.imat_iter) Inactive (metworkpy.imat.imat_iter.ReactionActivity attribute)

J

js_divergence() (in module metworkpy.divergence.js_divergence_functions)

js_divergence_array() (in module metworkpy.divergence.js_divergence_functions)

K

kl_divergence() (in module metworkpy.divergence.kl_divergence_functions)

kl_divergence_array() (in module metworkpy.divergence.kl_divergence_functions) ko_divergence() (in module metworkpy.divergence.ko_divergence_functions)

M

MannWhitneyUResult (class in metworkpy.utils.statistics) membership_distance_weighted_gene_density() (in module metworkpy.network.fuzzy) membership_distance_weighted_reaction_density() (in module metworkpy.network.fuzzy) membership_gene_enrichment() (in module metworkpy.network.fuzzy) membership_knn_gene_distance() (in module metworkpy.network.fuzzy) membership_knn_reaction_distance() (in module metworkpy.network.fuzzy) membership_simple_gene_density() (in module metworkpy.network.fuzzy) membership_simple_reaction_density() (in module metworkpy.network.fuzzy) metchange() (in module metworkpy.metabolites.metchange_functions) metworkpy.divergence.group_divergence module metworkpy.divergence.js_divergence_functions module metworkpy.divergence.kl_divergence_functions module metworkpy.divergence.ko_divergence_functions module metworkpy.gpr.gpr_functions module metworkpy.imat.imat_functions module metworkpy.imat.imat_iter module metworkpy.imat.model_creation module metworkpy.information.mutual_information_functions module metworkpy.information.mutual_information_network module metworkpy.metabolites.metabolite_network module metworkpy.metabolites.metchange_functions module metworkpy.network.centrality module metworkpy.network.components module metworkpy.network.density module metworkpy.network.fuzzy module metworkpy.network.neighborhoods module metworkpy.network.network_construction module metworkpy.network.projection module metworkpy.sampling.corners module metworkpy.sampling.diagnostics module metworkpy.sampling.upsampling module

metworkpy.synleth.fastess module metworkpy.synleth.fastsl module metworkpy.utils.connected_components module metworkpy.utils.expression_utils module metworkpy.utils.models module metworkpy.utils.permutation module metworkpy.utils.statistics module metworkpy.utils.translate module mi_network_adjacency_matrix() (in module metworkpy.information.mutual_information_network) mi_pairwise() (in module metworkpy.information.mutual_information_network) mi_pairwise_grouped() (in module metworkpy.information.mutual_information_network) milp_model() (in module metworkpy.imat.model_creation) model_bounds_eq() (in module metworkpy.utils.models) model_eq() (in module metworkpy.utils.models) module metworkpy.divergence.group_divergence metworkpy.divergence.js_divergence_functions metworkpy.divergence.kl_divergence_functions metworkpy.divergence.ko_divergence_functions metworkpy.gpr.gpr_functions metworkpy.imat.imat_functions metworkpy.imat.imat_iter metworkpy.imat.model_creation metworkpy.information.mutual_information_functions metworkpy.information.mutual_information_network metworkpy.metabolites.metabolite_network metworkpy.metabolites.metchange_functions metworkpy.network.centrality metworkpy.network.components metworkpy.network.density metworkpy.network.fuzzy metworkpy.network.neighborhoods metworkpy.network.network_construction metworkpy.network.projection metworkpy.sampling.corners metworkpy.sampling.diagnostics metworkpy.sampling.upsampling metworkpy.synleth.fastess metworkpy.synleth.fastsl metworkpy.utils.connected_components metworkpy.utils.expression_utils metworkpy.utils.models metworkpy.utils.permutation metworkpy.utils.statistics metworkpy.utils.translate mutual_information() (in module metworkpy.information.mutual_information_functions)

N

node_target_density() (in module metworkpy.network.density)

O

Other (metworkpy.imat.imat_iter.ReactionActivity attribute)

P

permutation_test() (in module metworkpy.utils.permutation)

pvalue (metworkpy.utils.statistics.MannWhitneyUResult attribute) (metworkpy.utils.statistics.SignificanceResult attribute)

R

reaction_to_gene_ids() (in module metworkpy.utils.translate) reaction_to_gene_list() (in module metworkpy.utils.translate) ReactionActivity (class in metworkpy.imat.imat_iter) read_model() (in module metworkpy.utils.models)

rh_y_neg (metworkpy.imat.imat_iter.ImatBinaryVariables attribute) rh_y_pos (metworkpy.imat.imat_iter.ImatBinaryVariables attribute) rl_y_pos (metworkpy.imat.imat_iter.ImatBinaryVariables attribute) rpkm_to_tpm() (in module metworkpy.utils.expression_utils)

S

SignificanceResult (class in metworkpy.utils.statistics) simple_bounds_model() (in module metworkpy.imat.model_creation)

statistic (metworkpy.utils.statistics.SignificanceResult attribute) subset_model() (in module metworkpy.imat.model_creation)

U

u1 (metworkpy.utils.statistics.MannWhitneyUResult attribute)

u2 (metworkpy.utils.statistics.MannWhitneyUResult attribute) upsample() (in module metworkpy.sampling.upsampling)

W

weight_fn_distr() (in module metworkpy.network.fuzzy) weight_fn_geom_series() (in module metworkpy.network.fuzzy)

weight_fn_poisson() (in module metworkpy.network.fuzzy) weight_fn_reciprocal() (in module metworkpy.network.fuzzy) write_model() (in module metworkpy.utils.models)