Index _ | A | C | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V _ __init__() (pymantra.database.APINetworkGenerator method) (pymantra.database.IncorrectEdgeType method) (pymantra.database.IncorrectNodeType method) (pymantra.database.NetworkGenerator method) (pymantra.EnrichmentResults method) (pymantra.MetaboliteLocalSearch method) (pymantra.MultiOmicsLocalSearch method) (pymantra.namemapping.ChEBIQuery method) (pymantra.namemapping.HMDBQuery method) (pymantra.namemapping.MantraDBQuery method) (pymantra.namemapping.NameMapper method) (pymantra.namemapping.ReactomeQuery method) (pymantra.namemapping.UnknownMappingError method) (pymantra.network.NodeTypeError method) A active_connection() (pymantra.namemapping.ChEBIQuery method) (pymantra.namemapping.HMDBQuery method) (pymantra.namemapping.MantraDBQuery method) (pymantra.namemapping.ReactomeQuery method) add_gene_associations() (in module pymantra.network) add_microbiome_associations() (in module pymantra.network) add_reaction_estimates() (in module pymantra.network) APINetworkGenerator (class in pymantra.database) as_networkx() (pymantra.database.APINetworkGenerator method) (pymantra.database.NetworkGenerator method) C chebi_to_internal() (pymantra.namemapping.MantraDBQuery method) ChEBIQuery (class in pymantra.namemapping) close() (pymantra.namemapping.NameMapper method) compute_multiomics_associations() (in module pymantra.network) compute_reaction_estimates() (in module pymantra.network) converged (pymantra.EnrichmentResults attribute) conversion_options (pymantra.namemapping.NameMapper property) E Edge (class in pymantra.statics) edges (pymantra.database.NetworkGenerator property) EnrichmentResults (class in pymantra) F from_json() (pymantra.EnrichmentResults class method) G gene_ids (pymantra.database.NetworkGenerator property) get_all_edges() (pymantra.database.NetworkGenerator method) get_gene_metabolite_connections() (pymantra.database.NetworkGenerator method) get_metabolite_metabolite_connection() (pymantra.database.NetworkGenerator method) get_node_attributes() (pymantra.database.NetworkGenerator method) get_node_by_id() (pymantra.database.NetworkGenerator method) get_node_edges() (pymantra.database.NetworkGenerator method) get_node_neighbours() (pymantra.database.NetworkGenerator method) get_organism_metabolite_connections() (pymantra.database.NetworkGenerator method) get_reaction_subgraph() (pymantra.database.APINetworkGenerator method) (pymantra.database.NetworkGenerator method) get_subgraph() (pymantra.database.APINetworkGenerator method) (pymantra.database.NetworkGenerator method) H hmdb_to_internal() (pymantra.namemapping.MantraDBQuery method) HMDBQuery (class in pymantra.namemapping) I inchi_to_internal() (pymantra.namemapping.NameMapper method) inchi_to_reactome() (pymantra.namemapping.NameMapper method) IncorrectEdgeType (class in pymantra.database) IncorrectNodeType (class in pymantra.database) K kegg_to_internal() (pymantra.namemapping.MantraDBQuery method) kegg_to_reactome() (pymantra.namemapping.NameMapper method) L lso (pymantra.MetaboliteLocalSearch attribute) (pymantra.MultiOmicsLocalSearch attribute) M MantraDBQuery (class in pymantra.namemapping) map_data() (pymantra.namemapping.NameMapper method) map_id() (pymantra.namemapping.NameMapper method) map_to_many() (pymantra.namemapping.NameMapper method) metabolite_ids (pymantra.database.NetworkGenerator property) MetaboliteLocalSearch (class in pymantra) module pymantra.plotting multi_taxonomy_from_foreign_id() (pymantra.namemapping.HMDBQuery method) MultiOmicsLocalSearch (class in pymantra) N n_edges (pymantra.database.NetworkGenerator property) n_nodes (pymantra.database.NetworkGenerator property) NameMapper (class in pymantra.namemapping) neo4j_nodes (pymantra.database.NetworkGenerator property) NetworkGenerator (class in pymantra.database) nodes (pymantra.database.NetworkGenerator property) NodeTypeError (class in pymantra.network) O organism_ids (pymantra.database.NetworkGenerator property) P per_sample_ld_estimation() (in module pymantra.network) plot_correlation_averages() (in module pymantra.plotting) plot_correlation_differences() (in module pymantra.plotting) plot_directed_graph() (in module pymantra.plotting) plot_reaction_association() (in module pymantra.plotting) plot_score_progression() (pymantra.LocalSearch method) plot_subnetwork() (pymantra.MetaboliteLocalSearch method) (pymantra.MultiOmicsLocalSearch method) plot_undirected_graph() (in module pymantra.plotting) print_conversion_options() (pymantra.namemapping.NameMapper method) pymantra.plotting module R reaction_edges (pymantra.MetaboliteLocalSearch attribute) reaction_graph_extraction() (in module pymantra.network) reaction_ids (pymantra.database.NetworkGenerator property) reaction_multiomics_edges (pymantra.MultiOmicsLocalSearch attribute) reactome_to_inchi() (pymantra.namemapping.NameMapper method) reactome_to_internal() (pymantra.namemapping.MantraDBQuery method) reactome_to_kegg() (pymantra.namemapping.NameMapper method) ReactomeQuery (class in pymantra.namemapping) reduce_reaction_nodes() (in module pymantra.database) residual_violinplot() (in module pymantra.plotting) S score (pymantra.EnrichmentResults attribute) set_l_max() (pymantra.LocalSearch method) set_l_min() (pymantra.LocalSearch method) set_max_iter() (pymantra.LocalSearch method) set_min_reactions() (pymantra.LocalSearch method) set_temp() (pymantra.LocalSearch method) source (pymantra.statics.Edge attribute), [1] spearmans_correlation() (in module pymantra.network) subgraph (pymantra.EnrichmentResults attribute) T target (pymantra.statics.Edge attribute), [1] taxonomy_from_foreign_id() (pymantra.namemapping.HMDBQuery method) U UnknownMappingError (class in pymantra.namemapping) url (pymantra.database.APINetworkGenerator attribute) V verify_connection() (pymantra.database.APINetworkGenerator method) vmh_to_internal() (pymantra.namemapping.MantraDBQuery method)