Index

Symbols

--allow-fallback napistu-integrate-dogmatic_scaffold command line option napistu-integrate-omnipath command line option napistu-integrate-reactome_fi command line option napistu-refine-expand_identifiers command line option --deduplicate_edges napistu-exporter-export_napistu_graph command line option --directed napistu-exporter-export_napistu_graph command line option --drop_reactions_when napistu-exporter-export_napistu_graph command line option --exchange-compartment napistu-refine-add_transportation_reactions command line option --format napistu-exporter-export_napistu_graph command line option napistu-exporter-export_precomputed_distances command line option --graph_attrs_spec_uri napistu-exporter-export_napistu_graph command line option --identifiers_df_uri napistu-helpers-validate_assets command line option --ignore-mergeability napistu-consensus-create command line option --is-file napistu-helpers-copy_uri command line option --max_score_q napistu-exporter-export_precomputed_distances command line option --max_steps napistu-exporter-export_precomputed_distances command line option --model-prefix napistu-exporter-export_smbl_dfs_tables command line option --napistu_graph_uri napistu-helpers-validate_assets command line option --nondogmatic napistu-consensus-create command line option napistu-exporter-export_smbl_dfs_tables command line option --ontologies napistu-refine-expand_identifiers command line option --overwrite napistu-exporter-export_smbl_dfs_tables command line option napistu-ingestion-bigg command line option napistu-ingestion-intact command line option napistu-ingestion-reactome command line option napistu-ingestion-reactome_fi command line option napistu-integrate-bigg command line option napistu-integrate-intact command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option napistu-integrate-reactome_fi command line option napistu-integrate-string_db command line option napistu-integrate-trrust command line option --partition_size napistu-exporter-export_precomputed_distances command line option --permissive napistu-integrate-reactome command line option --precomputed_distances_uri napistu-helpers-validate_assets command line option --preferred-method napistu-integrate-dogmatic_scaffold command line option napistu-integrate-omnipath command line option napistu-integrate-reactome_fi command line option napistu-refine-expand_identifiers command line option --reverse napistu-exporter-export_napistu_graph command line option --url napistu-ingestion-gtex-rnaseq-expression command line option napistu-ingestion-proteinatlas_subcell command line option napistu-ingestion-reactome_fi command line option --verbose napistu-integrate-reactome command line option --verbosity napistu-consensus-check command line option napistu-consensus-create command line option napistu-exporter-export_smbl_dfs_tables command line option napistu-helpers-copy_uri command line option napistu-helpers-summarize_sbml_dfs command line option napistu-helpers-validate_assets command line option napistu-helpers-validate_sbml_dfs command line option napistu-importer-sbml command line option napistu-importer-sbml_dfs command line option napistu-ingestion-bigg command line option napistu-ingestion-gtex-rnaseq-expression command line option napistu-ingestion-intact command line option napistu-ingestion-proteinatlas_subcell command line option napistu-ingestion-reactome command line option napistu-ingestion-reactome_fi command line option napistu-ingestion-string_aliases command line option napistu-ingestion-string_db command line option napistu-ingestion-trrust command line option napistu-integrate-bigg command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-intact command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option napistu-integrate-reactome_fi command line option napistu-integrate-string_db command line option napistu-integrate-trrust command line option napistu-refine-add_transportation_reactions command line option napistu-refine-filter_gtex_tissue command line option napistu-refine-filter_hpa_compartments command line option

--weight_vars napistu-exporter-export_precomputed_distances command line option --weighting_strategy napistu-exporter-export_napistu_graph command line option --wiring_approach napistu-exporter-export_napistu_graph command line option -a napistu-exporter-export_napistu_graph command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-omnipath command line option napistu-integrate-reactome_fi command line option napistu-refine-expand_identifiers command line option -d napistu-exporter-export_napistu_graph command line option napistu-helpers-validate_assets command line option -e napistu-refine-add_transportation_reactions command line option -f napistu-exporter-export_napistu_graph command line option napistu-exporter-export_precomputed_distances command line option -g napistu-exporter-export_napistu_graph command line option napistu-helpers-validate_assets command line option -i napistu-helpers-validate_assets command line option -m napistu-exporter-export_smbl_dfs_tables command line option -n napistu-consensus-create command line option napistu-exporter-export_smbl_dfs_tables command line option -o napistu-refine-expand_identifiers command line option -p napistu-exporter-export_precomputed_distances command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option napistu-integrate-reactome_fi command line option napistu-refine-expand_identifiers command line option -q napistu-exporter-export_precomputed_distances command line option -r napistu-exporter-export_napistu_graph command line option -s napistu-exporter-export_precomputed_distances command line option -v napistu-consensus-check command line option napistu-consensus-create command line option napistu-exporter-export_smbl_dfs_tables command line option napistu-helpers-copy_uri command line option napistu-helpers-summarize_sbml_dfs command line option napistu-helpers-validate_assets command line option napistu-helpers-validate_sbml_dfs command line option napistu-importer-sbml command line option napistu-importer-sbml_dfs command line option napistu-ingestion-bigg command line option napistu-ingestion-gtex-rnaseq-expression command line option napistu-ingestion-intact command line option napistu-ingestion-proteinatlas_subcell command line option napistu-ingestion-reactome command line option napistu-ingestion-reactome_fi command line option napistu-ingestion-string_aliases command line option napistu-ingestion-string_db command line option napistu-ingestion-trrust command line option napistu-integrate-bigg command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-intact command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option, [1] napistu-integrate-reactome_fi command line option napistu-integrate-string_db command line option napistu-integrate-trrust command line option napistu-refine-add_transportation_reactions command line option napistu-refine-filter_gtex_tissue command line option napistu-refine-filter_hpa_compartments command line option -w napistu-exporter-export_napistu_graph command line option napistu-exporter-export_precomputed_distances command line option -x napistu-exporter-export_napistu_graph command line option

_

__init__() (napistu.context.discretize.PeakSelector method) (napistu.genomics.gsea.GenesetCollection method) (napistu.genomics.scverse_loading.DatasetsConfig method) (napistu.identifiers.Identifiers method) (napistu.indices.PWIndex method) (napistu.ingestion.organismal_species.OrganismalSpeciesValidator method) (napistu.ingestion.sbml.SBML method) (napistu.ingestion.sbml.SBML_reaction method) (napistu.network.edgelist.Edgelist method) (napistu.network.net_propagation.PropagationMethod method) (napistu.network.ng_core.NapistuGraph method) (napistu.ontologies.genodexito.Genodexito method) (napistu.sbml_dfs_core.SBML_dfs method) (napistu.source.Source method) (napistu.utils.docker_utils.DockerImageManager method) (napistu.utils.match_pd_vars method) (napistu.utils.pd_utils.match_pd_vars method) _abc_impl (napistu.gcs.assets.GCSAsset attribute) (napistu.gcs.assets.GCSAssets attribute) (napistu.genomics.gsea.GmtsConfig attribute) (napistu.genomics.scverse_loading.DatasetConfig attribute) (napistu.genomics.scverse_loading.ModalityOntologyConfig attribute) (napistu.genomics.scverse_loading.MultiModalityOntologyConfig attribute) (napistu.identifiers._IdentifiersValidator attribute) (napistu.identifiers._IdentifierValidator attribute) (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) (napistu.ingestion.sbml.CompartmentAliasesValidator attribute) (napistu.modify.cofactors.CofactorChebiIDs attribute) (napistu.modify.cofactors.CofactorFilterRule attribute) (napistu.modify.cofactors.CofactorSchema attribute) (napistu.network.ng_utils._EntityAttrValidator attribute) (napistu.utils.docker_utils.DockerImageManager attribute) (napistu.utils.docker_utils.ImageInfo attribute) _add_attributes_df() (napistu.network.ng_core.NapistuGraph method) _add_complex_formation_compartmentalized_species() (in module napistu.modify.pathwayannot) _add_consensus_sources() (in module napistu.consensus) _add_edgelist_defaults() (in module napistu.sbml_dfs_utils) _add_entity_data (napistu.network.ng_core.NapistuGraph attribute) _add_entity_data() (in module napistu.consensus) (napistu.network.ng_core.NapistuGraph method) _add_entity_foreign_keys() (in module napistu.modify.curation) _add_entity_identifiers() (in module napistu.modify.curation) _add_entity_labels() (in module napistu.modify.curation) _add_entity_primary_keys() (in module napistu.modify.curation) _add_entity_sets_reactions() (in module napistu.modify.pathwayannot) _add_entity_sets_species() (in module napistu.modify.pathwayannot) _add_entity_sources() (in module napistu.modify.curation) _add_graph_weights_mixed (napistu.network.ng_core.NapistuGraph attribute) _add_graph_weights_mixed() (napistu.network.ng_core.NapistuGraph method) _add_nameness_score() (in module napistu.utils.string_utils) _add_nameness_score_wrapper() (in module napistu.utils.string_utils) _add_new_exchange_cspecies() (in module napistu.modify.gaps) _add_stoi_to_species_name() (in module napistu.sbml_dfs_utils) _aggregate_grouped_columns() (in module napistu.matching.mount) _allocate_samples_across_attributes() (in module napistu.network.net_propagation) _apply_cofactor_filters() (in module napistu.modify.cofactors) _apply_custom_loaders() (in module napistu.ingestion.harmonizome) _apply_edge_reversal_mapping() (in module napistu.network.ng_core) _apply_filters_to_reaction() (in module napistu.modify.cofactors) _apply_reaction_edge_multiplier (napistu.network.ng_core.NapistuGraph attribute) _apply_reaction_edge_multiplier() (napistu.network.ng_core.NapistuGraph method) _asdict() (napistu.context.discretize.PeakIndices method) _assert_quantile_inputs() (in module napistu.statistics.quantiles) _attempt_resolve (napistu.sbml_dfs_core.SBML_dfs attribute) _attempt_resolve() (napistu.sbml_dfs_core.SBML_dfs method) _attr_pooled_vertex_permutation_null() (in module napistu.network.net_propagation) _augment_network_edges() (in module napistu.network.net_create) _augment_network_nodes() (in module napistu.network.net_create) _binarize_species_data() (in module napistu.context.filtering) _build_consensus_identifiers() (in module napistu.consensus) _build_final_result() (in module napistu.network.neighborhoods) _build_interactor_edgelist() (in module napistu.ingestion.string) _build_pooled_universe() (in module napistu.network.net_propagation) _build_psi_mi_ontology_graph() (in module napistu.ingestion.intact) _build_raw_neighborhood_df() (in module napistu.network.neighborhoods) _build_reactome_pw_index() (in module napistu.ingestion.reactome) _build_species_df() (in module napistu.ingestion.string) _build_string_reaction_name() (in module napistu.ingestion.string) _build_transport_rxn_edgelist() (in module napistu.modify.gaps) _calculate_all_scores_vectorized() (in module napistu.ingestion.intact) _calculate_category_scores_vectorized() (in module napistu.ingestion.intact) _calculate_distances_subset() (in module napistu.network.precompute) _calculate_enrichment_statistics() (in module napistu.genomics.gsea) _calculate_geneset_edge_counts() (in module napistu.genomics.gsea) _calculate_net_polarity() (in module napistu.network.paths) _calculate_path_attrs() (in module napistu.network.neighborhoods) _calculate_quantiles_dense() (in module napistu.statistics.quantiles) _calculate_quantiles_per_feature() (in module napistu.statistics.quantiles) _categorize_perturbseq_row() (in module napistu.ingestion.perturbseq) _check_files() (napistu.indices.PWIndex method) _check_mappings() (napistu.ontologies.genodexito.Genodexito method) _check_reactome_pw_index() (in module napistu.ingestion.reactome) _check_sbml_dfs() (in module napistu.consensus) _check_sbml_dfs_dict() (in module napistu.consensus) _check_sbml_dfs_mergeability() (in module napistu.consensus) _check_species_identifiers_table() (in module napistu.identifiers) _classify_columns_modify_types() (in module napistu.matching.mount) _clean_disconnected_components() (in module napistu.network.neighborhoods) _cleanup_removed_attributes_metadata() (napistu.network.ng_core.NapistuGraph method) _coerce_to_2d_null_block() (in module napistu.statistics.quantiles) _collapse_by_membership_string() (in module napistu.source) _collapse_source_df() (in module napistu.source) _compare_and_merge_attrs (napistu.network.ng_core.NapistuGraph attribute) _compare_and_merge_attrs() (napistu.network.ng_core.NapistuGraph method) _compute_log2_enrichment() (in module napistu.network.net_propagation) _configure_package_logging() (in module napistu.utils.optional) _connect_dogmatic_mappings() (in module napistu.ontologies.dogma) _contains (napistu.genomics.scverse_loading.DatasetsConfig attribute) _copy_tree() (in module napistu.utils.io_utils) _count_edges_by_geneset_pair_chunked() (in module napistu.genomics.gsea) _count_reactome_species() (in module napistu.ontologies.standardization) _count_studies_with_scored_attributes() (in module napistu.ingestion.intact) _create_alias_mapping() (in module napistu.ontologies.renaming) _create_basic_edgelist() (in module napistu.ingestion.intact) _create_cluster_identifiers() (in module napistu.consensus) _create_consensus_entities() (in module napistu.consensus) _create_consensus_entity_data() (in module napistu.consensus) _create_consensus_sources() (in module napistu.consensus) _create_consensus_table() (in module napistu.consensus) _create_cooccurence_edgelist() (in module napistu.context.filtering) _create_data_table_column_mapping() (in module napistu.network.data_handling) _create_deep_to_shallow_lookup() (napistu.genomics.gsea.GenesetCollection method) _create_default_consensus_source() (in module napistu.consensus) _create_entity_consensus() (in module napistu.consensus) _create_entity_lookup_table() (in module napistu.consensus) _create_expanded_identifiers() (napistu.ontologies.genodexito.Genodexito method) _create_gmt() (napistu.genomics.gsea.GenesetCollection method) _create_graph_attrs_config() (in module napistu.network.data_handling) _create_left_align_formatters() (in module napistu.utils.display_utils) _create_member_string() (in module napistu.consensus) _create_membership_lookup() (in module napistu.consensus) _create_mygene_mapping_tables() (in module napistu.ontologies.mygene) _create_napistu_graph_bipartite() (in module napistu.network.net_create) _create_neighborhood_dict_entry_logging() (in module napistu.network.neighborhoods) _create_new_reaction_species() (in module napistu.modify.gaps) _create_new_reactions() (in module napistu.modify.gaps) _create_r_identifiers() (in module napistu.ingestion.intact) _create_reaction_species_df() (in module napistu.ingestion.psi_mi) _create_results_df() (in module napistu.genomics.scverse_loading) _create_single_mapping() (in module napistu.rpy2.rids) _create_source_weights (napistu.network.ng_core.NapistuGraph attribute) _create_source_weights() (napistu.network.ng_core.NapistuGraph method) _create_species_df() (in module napistu.ingestion.intact) _create_stubbed_index() (in module napistu.modify.uncompartmentalize) _create_stubbed_source() (in module napistu.modify.uncompartmentalize) _create_study_species_df() (in module napistu.ingestion.psi_mi) _create_universe_edgelist() (in module napistu.network.ig_utils) _create_vertex_category() (in module napistu.consensus) _cv_to_Identifiers() (in module napistu.ingestion.sbml) _deduplicate_identifiers_by_priority() (in module napistu.identifiers) _deduplicate_source_df() (in module napistu.source) _default_loader() (napistu.ingestion.harmonizome.HarmonizomeDataset static method) _define_compartments() (napistu.ingestion.sbml.SBML method) _define_compartments_missing_cvterms() (in module napistu.ingestion.sbml) _define_cspecies() (napistu.ingestion.sbml.SBML method) _define_edgelist_df_ids_and_counts() (in module napistu.ingestion.intact) _define_fbc_gene_products() (napistu.ingestion.sbml.SBML method) _define_reactions() (napistu.ingestion.sbml.SBML method) _define_species() (napistu.ingestion.sbml.SBML method) _dogmatic_to_defining_bqbs() (in module napistu.sbml_dfs_utils) _edge_permutation_null() (in module napistu.network.net_propagation) _edgelist_assemble_sbml_model (napistu.sbml_dfs_core.SBML_dfs attribute) _edgelist_assemble_sbml_model() (napistu.sbml_dfs_core.SBML_dfs class method) _edgelist_create_compartmentalized_species() (in module napistu.sbml_dfs_utils) _edgelist_create_reactions_and_species() (in module napistu.sbml_dfs_utils) _edgelist_identify_extra_columns() (in module napistu.sbml_dfs_utils) _edgelist_process_compartments() (in module napistu.sbml_dfs_utils) _edgelist_process_species() (in module napistu.sbml_dfs_utils) _edgelist_to_scids_if_needed() (in module napistu.matching.interactions) _edgelist_validate_inputs() (in module napistu.sbml_dfs_utils) _ensure_feature_id_var() (in module napistu.matching.species) _ensure_propagation_method() (in module napistu.network.net_propagation) _ensure_source_total_counts() (in module napistu.source) _ensure_valid_attribute() (in module napistu.network.ig_utils) _EntityAttrValidator (class in napistu.network.ng_utils) _eval_existing_inter_cspecies_paths() (in module napistu.modify.gaps) _expand_entities_by_fks() (in module napistu.modify.curation) _extract_gene_products() (in module napistu.ingestion.sbml) _extract_omnipath_identifiers() (in module napistu.ingestion.omnipath) _extract_ontologies() (in module napistu.genomics.scverse_loading) _extract_tarball() (in module napistu.utils.io_utils) _extract_zip() (in module napistu.utils.io_utils) _fetch_batch() (in module napistu.ontologies.pubchem) _fetch_individual_cids() (in module napistu.ontologies.pubchem) _fetch_mygene_data() (in module napistu.ontologies.mygene) _fetch_mygene_data_all_queries() (in module napistu.ontologies.mygene) _field_defaults (napistu.context.discretize.PeakIndices attribute) _fields (napistu.context.discretize.PeakIndices attribute) _filter_genesets_to_universe() (in module napistu.genomics.gsea) _filter_identifiers_by_qualifier() (in module napistu.consensus) _filter_intact_xrefs() (in module napistu.ingestion.intact) _filter_one_reactions_cofactors() (in module napistu.modify.cofactors) _filter_paths_by_precomputed_distances() (in module napistu.network.paths) _filter_precomputed_distances() (in module napistu.network.precompute) _filter_promiscuous_components() (in module napistu.sbml_dfs_utils) _filter_to_pathways() (in module napistu.sbml_dfs_utils) _filter_trivial_reactions() (in module napistu.modify.uncompartmentalize) _find_cofactor_species() (in module napistu.modify.cofactors) _find_existing_inter_cspecies_paths() (in module napistu.modify.gaps) _find_invalid_entities() (in module napistu.modify.curation) _find_invalid_entities_by_reference (napistu.sbml_dfs_core.SBML_dfs attribute) _find_invalid_entities_by_reference() (napistu.sbml_dfs_core.SBML_dfs method) _find_neighbors() (in module napistu.network.neighborhoods) _find_neighbors_paths() (in module napistu.network.neighborhoods) _find_new_exchange_cspecies() (in module napistu.modify.gaps) _find_obo_attrib_dups() (in module napistu.ingestion.obo) _find_reactions_by_relationship() (in module napistu.network.neighborhoods) _find_reactions_with_disconnected_cspecies() (in module napistu.context.filtering) _find_sbo_duos() (in module napistu.network.net_create_utils) _find_underspecified_reactions() (in module napistu.sbml_dfs_utils) _find_underspecified_reactions_by_reference (napistu.sbml_dfs_core.SBML_dfs attribute) _find_underspecified_reactions_by_reference() (napistu.sbml_dfs_core.SBML_dfs method) _find_unique_weight_vars() (in module napistu.network.precompute) _fit_distribution_parameters() (in module napistu.network.net_propagation) _fix_consensus_logic() (in module napistu.ingestion.omnipath) _format_complex_interactions() (in module napistu.ingestion.omnipath) _format_cross_tier_edges() (in module napistu.network.net_create_utils) _format_edgelist_interactions() (in module napistu.ingestion.omnipath) _format_entry() (in module napistu.ingestion.psi_mi) _format_entry_experiment() (in module napistu.ingestion.psi_mi) _format_entry_interaction() (in module napistu.ingestion.psi_mi) _format_entry_interaction_participants() (in module napistu.ingestion.psi_mi) _format_entry_interactions() (in module napistu.ingestion.psi_mi) _format_entry_interactor() (in module napistu.ingestion.psi_mi) _format_entry_interactor_list() (in module napistu.ingestion.psi_mi) _format_entry_interactor_xrefs() (in module napistu.ingestion.psi_mi) _format_entry_source() (in module napistu.ingestion.psi_mi) _format_entry_tuple() (in module napistu.ingestion.obo) _format_explicit_reaction_species() (in module napistu.modify.curation) _format_gmts_config() (napistu.genomics.gsea.GenesetCollection method) _format_harmonizome_replogle_with_species_ids() (in module napistu.ingestion.perturbseq) _format_Identifiers_pubmed() (in module napistu.ontologies.standardization) _format_implicit_reaction_species() (in module napistu.modify.curation) _format_mygene_fields() (in module napistu.ontologies.mygene) _format_mygene_species() (in module napistu.ontologies.mygene) _format_perturbatalas_perturbations() (in module napistu.ingestion.harmonizome) _format_perturbatlas_with_species_ids() (in module napistu.ingestion.perturbseq) _format_pubmed_for_interactions() (in module napistu.ingestion.trrust) _format_reaction_references() (in module napistu.ingestion.omnipath) _format_same_tier_edges() (in module napistu.network.net_create_utils) _format_study_level_data() (in module napistu.ingestion.psi_mi) _format_tier_combo() (in module napistu.network.net_create_utils) _generate_parametric_null_sample() (in module napistu.network.net_propagation) _get_attribute_masks() (in module napistu.network.ig_utils)

_get_biological_qualifier_codes() (in module napistu.ingestion.sbml) _get_boolean_aggregator() (in module napistu.matching.mount) _get_data_summary() (napistu.sbml_dfs_core.SBML_dfs method) _get_distinct_harmonizome_perturbseq_interactions() (in module napistu.ingestion.perturbseq) _get_distinct_replogle_pvalues() (in module napistu.ingestion.perturbseq) _get_distribution_object() (in module napistu.network.net_propagation) _get_engine_from_string() (in module napistu.genomics.gsea) _get_entity_attrs (napistu.network.ng_core.NapistuGraph attribute) _get_entity_attrs() (napistu.network.ng_core.NapistuGraph method) _get_entity_data (napistu.sbml_dfs_core.SBML_dfs attribute) _get_entity_data() (napistu.sbml_dfs_core.SBML_dfs method) _get_gcs_asset_path() (in module napistu.gcs.downloads) _get_gene_product_dict() (in module napistu.ingestion.sbml) _get_human_symbol_to_entrez_mapping() (in module napistu.ingestion.reactome_fi) _get_identifiers() (in module napistu.ingestion.string) _get_identifiers_table_for_ontology_occurrence (napistu.sbml_dfs_core.SBML_dfs attribute) _get_identifiers_table_for_ontology_occurrence() (napistu.sbml_dfs_core.SBML_dfs method) _get_intact_scored_term() (in module napistu.ingestion.intact) _get_intact_species_basename() (in module napistu.ingestion.intact) _get_intact_term_with_score() (in module napistu.ingestion.intact) _get_interaction_symbol() (in module napistu.sbml_dfs_utils) _get_item (napistu.genomics.scverse_loading.DatasetsConfig attribute) _get_no_rxn_pathway_ids() (in module napistu.consensus) _get_non_interactor_reactions (napistu.sbml_dfs_core.SBML_dfs attribute) _get_non_interactor_reactions() (napistu.sbml_dfs_core.SBML_dfs method) _get_null_generator() (in module napistu.network.net_propagation) _get_numeric_aggregator() (in module napistu.matching.mount) _get_omnipath_fxn_map() (in module napistu.ingestion.omnipath) _get_optional_attribute() (in module napistu.ingestion.psi_mi) _get_optional_text() (in module napistu.ingestion.psi_mi) _get_py2rpy_pandas_conv() (in module napistu.rpy2.callr) _get_reactome_fi_species_systematic_ids() (in module napistu.ingestion.reactome_fi) _get_reactome_pathway_list() (in module napistu.ingestion.reactome) _get_table_from_dict_attr() (in module napistu.genomics.scverse_loading) _get_top_n_component_stats() (in module napistu.network.ig_utils) _get_top_n_idx() (in module napistu.network.ig_utils) _get_top_n_nodes() (in module napistu.network.ig_utils) _get_top_n_objects() (in module napistu.network.ig_utils) _get_uniprot_2_symbol_mapping() (in module napistu.ingestion.trrust) _get_universe_degrees() (in module napistu.network.ig_utils) _get_universe_edge_filters() (in module napistu.network.ig_utils) _get_universe_vertex_names() (in module napistu.network.ig_utils) _get_valid_attrs_for_feature_level_array() (in module napistu.genomics.scverse_loading) _get_weight_variables (napistu.network.ng_core.NapistuGraph attribute) _get_weight_variables() (napistu.network.ng_core.NapistuGraph method) _get_wide_results_valid_ontologies() (in module napistu.matching.mount) _handle_entries_without_identifiers() (in module napistu.consensus) _handle_special_reversal_cases() (in module napistu.network.ng_core) _id_dict_to_df() (in module napistu.sbml_dfs_utils) _IdentifiersValidator (class in napistu.identifiers) _IdentifierValidator (class in napistu.identifiers) _identify_species_needing_transport_reactions() (in module napistu.modify.gaps) _in_jupyter_environment() (in module napistu.utils.display_utils) _infer_primary_reactome_species() (in module napistu.ontologies.standardization) _initialize_data_dir() (in module napistu.gcs.utils) _interactor_duos_to_wide() (in module napistu.network.net_create_utils) _is_immediate_failure() (in module napistu.ontologies.pubchem) _isa_str_list_to_dict_list() (in module napistu.ingestion.obo) _label_path_reactions() (in module napistu.network.paths) _libsbml() (in module napistu.ingestion.sbml) _load_achilles_interactions() (in module napistu.ingestion.harmonizome) _load_clinvar_interactions() (in module napistu.ingestion.harmonizome) _load_dbgap_interactions() (in module napistu.ingestion.harmonizome) _load_drugbank_attributes() (in module napistu.ingestion.harmonizome) _load_drugbank_interactions() (in module napistu.ingestion.harmonizome) _load_gad_interactions() (in module napistu.ingestion.harmonizome) _load_omnipath_attribute_mapper() (in module napistu.ingestion.omnipath) _load_perturbatlas_interactions() (in module napistu.ingestion.harmonizome) _load_raw_table() (in module napistu.genomics.scverse_loading) _load_replogle_interactions() (in module napistu.ingestion.harmonizome) _log_edgelist_ora_input() (in module napistu.genomics.gsea) _log_edgelist_ora_paired_counts() (in module napistu.genomics.gsea) _log_edgelist_ora_paired_results() (in module napistu.genomics.gsea) _log_edgelist_ora_universe() (in module napistu.genomics.gsea) _log_feature_species_mapping_stats() (in module napistu.matching.species) _log_invalid_primary_refs() (in module napistu.ingestion.intact) _log_ontology_updates() (in module napistu.ontologies.renaming) _log_pathological_same_tier() (in module napistu.network.net_create_utils) _log_protein_transport_gapfilling() (in module napistu.modify.gaps) _make() (napistu.context.discretize.PeakIndices class method) _map_cofactors_to_reaction_species() (in module napistu.modify.cofactors) _map_sbo_identifiers() (in module napistu.rpy2.constants) _merge_and_log_overwrites() (in module napistu.utils.pd_utils) _merge_entity_data() (in module napistu.consensus) _merge_entity_data_create_consensus() (in module napistu.consensus) _merge_entity_data_report_mismatches() (in module napistu.consensus) _merge_entity_identifiers() (in module napistu.consensus) _merge_propagation_null_run_outputs() (in module napistu.network.net_propagation) _merge_reactome_crossref_ids() (in module napistu.modify.pathwayannot) _name_interaction() (in module napistu.sbml_dfs_utils) _name_interactions() (in module napistu.ingestion.omnipath) _netloc_to_identifiers_matrixdb_adaptor() (in module napistu.ontologies.standardization) _netloc_to_identifiers_mirbase_adaptor() (in module napistu.ontologies.standardization) _netloc_to_identifiers_pubchem_adaptor() (in module napistu.ontologies.standardization) _netloc_w_url_prefix_to_identifiers_ncbi_adaptor() (in module napistu.ontologies.standardization) _netloc_w_url_suffix_to_identifiers_ensembl_adaptor() (in module napistu.ontologies.standardization) _netloc_w_url_suffix_to_identifiers_phosphosite_adaptor() (in module napistu.ontologies.standardization) _optional_entities (napistu.sbml_dfs_core.SBML_dfs attribute) _pagerank_wrapper() (in module napistu.network.net_propagation) _parametric_null() (in module napistu.network.net_propagation) _parse_mask_input() (in module napistu.network.ig_utils) _parse_omnipath_annotation() (in module napistu.ingestion.omnipath) _parse_omnipath_named_annotation() (in module napistu.ingestion.omnipath) _parse_reactome_fi_annotations() (in module napistu.ingestion.reactome_fi) _patch() (in module napistu.network.paths) _patch_degenerate_s_names() (in module napistu.ingestion.omnipath) _perform_sbml_dfs_table_validation() (in module napistu.sbml_dfs_utils) _pooled_vertex_permutation_null() (in module napistu.network.net_propagation) _pre_consensus_compartment_check() (in module napistu.consensus) _pre_consensus_ontology_check() (in module napistu.consensus) _precompute_neighbors() (in module napistu.network.neighborhoods) _prepare_consensus_table() (in module napistu.consensus) _prepare_identifier_edgelist() (in module napistu.consensus) _prepare_integer_based_ids() (in module napistu.ingestion.omnipath) _prepare_member_table() (in module napistu.consensus) _prepare_omnipath_ids_complexes() (in module napistu.ingestion.omnipath) _prepare_omnipath_ids_mirbase() (in module napistu.ingestion.omnipath) _prepare_omnipath_ids_uniprot() (in module napistu.ingestion.omnipath) _prepare_species_identifiers() (in module napistu.identifiers) _print_mask_input_result() (in module napistu.network.ig_utils) _process_batch_response() (in module napistu.ontologies.pubchem) _process_ensembl_ids() (in module napistu.ingestion.intact) _process_path_information() (in module napistu.network.neighborhoods) _process_source_df() (napistu.source.Source method) _propagate_and_broadcast() (in module napistu.network.net_propagation) _prune_vertex_set() (in module napistu.network.neighborhoods) _r_homer_warning() (in module napistu.rpy2) _reaction_species_to_tiers() (in module napistu.network.net_create_utils) _reactome_id_species() (in module napistu.ontologies.standardization) _read_neo4j_members() (in module napistu.modify.pathwayannot) _read_reactome_crossref_ids() (in module napistu.modify.pathwayannot) _read_string() (in module napistu.ingestion.string) _read_string_aliases() (in module napistu.ingestion.string) _read_trrust() (in module napistu.ingestion.trrust) _reduce_to_consensus_ids() (in module napistu.consensus) _refine_compartments() (in module napistu.ingestion.sbml) _reformat_obo_entry_as_dict() (in module napistu.ingestion.obo) _remove_asset_files_if_needed() (in module napistu.gcs.downloads) _remove_entities() (in module napistu.modify.curation) _remove_entities_direct (napistu.sbml_dfs_core.SBML_dfs attribute) _remove_entities_direct() (napistu.sbml_dfs_core.SBML_dfs method) _remove_entity_data (napistu.sbml_dfs_core.SBML_dfs attribute) _remove_entity_data() (napistu.sbml_dfs_core.SBML_dfs method) _remove_nan_inf_rows() (in module napistu.context.discretize) _remove_no_rxn_pathways() (in module napistu.consensus) _replace() (napistu.context.discretize.PeakIndices method) _report_consensus_merges() (in module napistu.consensus) _required_entities (napistu.sbml_dfs_core.SBML_dfs attribute) _resolve_edgelist() (in module napistu.genomics.gsea) _resolve_reversibility() (in module napistu.consensus) _restore_logging() (in module napistu.utils.optional) _reverse_network_edges() (in module napistu.network.net_create) _run_infomap_local() (in module napistu.network.clustering) _run_infomap_subprocess() (in module napistu.network.clustering) _safe_source_merge() (in module napistu.source) _sanitize_id_table_bqbs() (in module napistu.ontologies.id_tables) _sanitize_id_table_identifiers() (in module napistu.ontologies.id_tables) _sanitize_id_table_ontologies() (in module napistu.ontologies.id_tables) _sanitize_id_table_values() (in module napistu.ontologies.id_tables) _sanitize_identifiers() (in module napistu.ingestion.intact) _sbml_dfs_from_edgelist_check_cspecies_merge() (in module napistu.sbml_dfs_utils) _select_priority_pathway_sources() (in module napistu.sbml_dfs_utils) _select_results_attrs() (in module napistu.genomics.scverse_loading) _select_sbml_dfs_data_table() (in module napistu.network.data_handling) _select_top_pathway_by_enrichment() (in module napistu.source) _select_top_pathway_by_size() (in module napistu.source) _setup_vertex_permutation_null() (in module napistu.network.net_propagation) _should_drop_reaction() (in module napistu.network.net_create_utils) _show_as_string() (in module napistu.utils.display_utils) _split_mdata_results_by_modality() (in module napistu.genomics.scverse_loading) _split_numeric_non_numeric_columns() (in module napistu.matching.mount) _split_one_to_identifiers_chebi_adaptor() (in module napistu.ontologies.standardization) _standardize_interaction_attrs() (in module napistu.ingestion.intact) _summarize_ontology_cooccurrence() (in module napistu.sbml_dfs_utils) _summarize_ontology_occurrence() (in module napistu.sbml_dfs_utils) _summarize_source_cooccurrence() (in module napistu.sbml_dfs_utils) _summarize_source_occurrence() (in module napistu.sbml_dfs_utils) _summarize_trrust_pairs() (in module napistu.ingestion.trrust) _terminal_net_polarity() (in module napistu.network.paths) _transform_entity_attributes() (napistu.network.ng_core.NapistuGraph method) _uncompartmentalize_cspecies() (in module napistu.modify.uncompartmentalize) _uncompartmentalize_reactions() (in module napistu.modify.uncompartmentalize) _uniform_null() (in module napistu.network.net_propagation) _unnest_SBML_df() (in module napistu.consensus) _update_foreign_keys() (in module napistu.consensus) _update_unaccounted_for_members() (in module napistu.source) _use_mappings() (napistu.ontologies.genodexito.Genodexito method) _validate_and_set_species (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) _validate_and_set_species() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator method) _validate_assets_graph_dist() (in module napistu.network.ng_utils) _validate_assets_sbml_graph() (in module napistu.network.ng_utils) _validate_assets_sbml_ids() (in module napistu.identifiers) _validate_bqb() (in module napistu.ontologies.standardization) _validate_consensus_table() (in module napistu.consensus) _validate_edgelist_consistency() (in module napistu.sbml_dfs_utils) _validate_edgelist_universe() (in module napistu.genomics.gsea) _validate_entity_attrs() (in module napistu.network.ng_utils) _validate_entity_data_access (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_entity_data_access() (napistu.sbml_dfs_core.SBML_dfs method) _validate_final_df() (napistu.source.Source method) _validate_format_curated_entities_inputs() (in module napistu.modify.curation) _validate_gcs_asset() (in module napistu.gcs.downloads) _validate_gcs_asset_version() (in module napistu.gcs.downloads) _validate_gcs_subasset() (in module napistu.gcs.downloads) _validate_id_table() (in module napistu.ontologies.id_tables) _validate_identifiers (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_identifiers() (napistu.sbml_dfs_core.SBML_dfs method) _validate_interactor_duos() (in module napistu.network.net_create_utils) _validate_masks_identical() (in module napistu.network.net_propagation) _validate_matching_data() (in module napistu.sbml_dfs_utils) _validate_merge_entity_data_create_consensus() (in module napistu.consensus) _validate_meta_identifiers() (in module napistu.consensus) _validate_neighborhood_consistency() (in module napistu.network.neighborhoods) _validate_non_null_values() (in module napistu.sbml_dfs_utils) _validate_params() (in module napistu.ontologies.pubchem) _validate_pathway_index() (napistu.source.Source method) _validate_pk_fk_correspondence (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_pk_fk_correspondence() (napistu.sbml_dfs_core.SBML_dfs method) _validate_precomputed_distances() (in module napistu.network.precompute) _validate_r_ids (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_r_ids() (napistu.sbml_dfs_core.SBML_dfs method) _validate_reaction_species (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_reaction_species() (napistu.sbml_dfs_core.SBML_dfs method) _validate_reactions_data (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_reactions_data() (napistu.sbml_dfs_core.SBML_dfs method) _validate_sbo_indexed_rsc_stoi() (in module napistu.network.net_create_utils) _validate_sbo_values() (in module napistu.sbml_dfs_utils) _validate_side_loaded_attributes() (in module napistu.network.ng_utils) _validate_source_df() (napistu.source.Source method) _validate_sources (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_sources() (napistu.sbml_dfs_core.SBML_dfs method) _validate_species_consistency() (in module napistu.ingestion.sbml) _validate_species_data (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_species_data() (napistu.sbml_dfs_core.SBML_dfs method) _validate_table (napistu.sbml_dfs_core.SBML_dfs attribute) _validate_table() (napistu.sbml_dfs_core.SBML_dfs method) _validate_vertex_attributes() (in module napistu.network.net_propagation) _validate_wide_ontologies() (in module napistu.matching.species) _verify_docker_available() (in module napistu.utils.docker_utils) _vertex_permutation_null() (in module napistu.network.net_propagation) _wt_transformation_identity() (in module napistu.network.ng_utils) _wt_transformation_string() (in module napistu.network.ng_utils) _wt_transformation_string_inv() (in module napistu.network.ng_utils) _zfpkm_calc() (in module napistu.context.discretize)

A

adapt_pw_index() (in module napistu.indices) add_all_entity_data() (napistu.network.ng_core.NapistuGraph method) add_complex_formation() (in module napistu.modify.pathwayannot) add_complex_formation_species() (in module napistu.modify.pathwayannot) add_degree_attributes (napistu.network.ng_core.NapistuGraph attribute) add_degree_attributes() (napistu.network.ng_core.NapistuGraph method) add_edge_data (napistu.network.ng_core.NapistuGraph attribute) add_edge_data() (napistu.network.ng_core.NapistuGraph method) add_entity_sets() (in module napistu.modify.pathwayannot) add_gmts (napistu.genomics.gsea.GenesetCollection attribute) add_gmts() (napistu.genomics.gsea.GenesetCollection method) add_missing_ids_column() (in module napistu.sbml_dfs_utils) add_reactions_data (napistu.sbml_dfs_core.SBML_dfs attribute) add_reactions_data() (napistu.sbml_dfs_core.SBML_dfs method) add_reactome_identifiers() (in module napistu.modify.pathwayannot) add_results_table_to_graph() (in module napistu.network.data_handling) add_sbml_dfs_summaries (napistu.network.ng_core.NapistuGraph attribute) add_sbml_dfs_summaries() (napistu.network.ng_core.NapistuGraph method) add_sbo_role() (in module napistu.sbml_dfs_utils)

add_species_data (napistu.sbml_dfs_core.SBML_dfs attribute) add_species_data() (napistu.sbml_dfs_core.SBML_dfs method) add_topology_weights (napistu.network.ng_core.NapistuGraph attribute) add_topology_weights() (napistu.network.ng_core.NapistuGraph method) add_transportation_reactions() (in module napistu.modify.gaps) add_vertex_data (napistu.network.ng_core.NapistuGraph attribute) add_vertex_data() (napistu.network.ng_core.NapistuGraph method) add_vertices_uri_urls() (in module napistu.network.neighborhoods) aggregate_psi_mis() (in module napistu.ingestion.psi_mi) apply_weight_transformations() (in module napistu.network.ng_utils) are_present (napistu.utils.match_pd_vars attribute) (napistu.utils.pd_utils.match_pd_vars attribute) as_substrate (napistu.modify.cofactors.CofactorFilterRule attribute) assert_present() (napistu.utils.match_pd_vars method), [1] (napistu.utils.pd_utils.match_pd_vars method), [1] assert_supported (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) assert_supported() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator method) assets (napistu.gcs.assets.GCSAssets attribute) assign_predicted_direction() (in module napistu.ingestion.perturbseq) auto_pull (napistu.utils.docker_utils.DockerImageManager attribute)

B

BASE_FOLDER napistu-ingestion-bigg command line option napistu-ingestion-reactome command line option base_path (napistu.indices.PWIndex attribute) bigg_sbml_download() (in module napistu.ingestion.bigg)

bind_dict_of_wide_results() (in module napistu.matching.mount) bind_wide_results() (in module napistu.matching.mount) binomial_test_vectorized() (in module napistu.statistics.hypothesis_testing) bioconductor_org_r_function() (in module napistu.rpy2.callr) bqb (napistu.identifiers._IdentifierValidator attribute) bucket (napistu.gcs.assets.GCSAssets attribute)

C

calculate_quantiles() (in module napistu.statistics.quantiles) categories (napistu.genomics.gsea.GmtsConfig attribute) check_entity_data_index_matching() (in module napistu.sbml_dfs_utils) check_reactome_identifier_compatibility() (in module napistu.ontologies.standardization) check_unique_index() (in module napistu.utils) (in module napistu.utils.pd_utils) cofactor_mapping (napistu.modify.cofactors.CofactorChebiIDs attribute) CofactorChebiIDs (class in napistu.modify.cofactors) CofactorFilterRule (class in napistu.modify.cofactors) CofactorSchema (class in napistu.modify.cofactors) common_name (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) (napistu.ingestion.organismal_species.OrganismalSpeciesValidator property) CompartmentAliasesValidator (class in napistu.ingestion.sbml) compartmentalize_species() (in module napistu.network.ng_utils) compartmentalize_species_pairs() (in module napistu.network.ng_utils) compartments (napistu.sbml_dfs_core.SBML_dfs attribute), [1] construct_bigg_consensus() (in module napistu.ingestion.bigg) construct_consensus_model() (in module napistu.consensus) construct_cspecies_identifiers() (in module napistu.identifiers) construct_formula_string() (in module napistu.sbml_dfs_utils) construct_meta_entities_fk() (in module napistu.consensus) construct_meta_entities_identifiers() (in module napistu.consensus) construct_meta_entities_members() (in module napistu.consensus) construct_reactome_consensus() (in module napistu.ingestion.reactome) construct_sbml_dfs_dict() (in module napistu.consensus) convert_reactome_fi_to_sbml_dfs() (in module napistu.ingestion.reactome_fi) convert_string_to_sbml_dfs() (in module napistu.ingestion.string) convert_trrust_to_sbml_dfs() (in module napistu.ingestion.trrust) copy (napistu.network.ng_core.NapistuGraph attribute) (napistu.sbml_dfs_core.SBML_dfs attribute) copy() (napistu.network.ng_core.NapistuGraph method) (napistu.sbml_dfs_core.SBML_dfs method)

copy_uri() (in module napistu.utils) (in module napistu.utils.path_utils) count_fraction_of_reciprocal_interactions() (in module napistu.ingestion.napistu_edgelist) create_bioconductor_mapping_tables() (in module napistu.rpy2.rids) create_dogmatic_sbml_dfs() (in module napistu.ontologies.dogma) create_entity_attrs_from_data_tables() (in module napistu.network.ng_utils) create_go_ancestors_df() (in module napistu.ingestion.obo) create_go_parents_df() (in module napistu.ingestion.obo) create_graph_hierarchy_df() (in module napistu.network.net_create_utils) create_induced_subgraph() (in module napistu.network.ig_utils) create_interaction_edgelist() (in module napistu.ingestion.reactome_fi) create_mapping_tables() (napistu.ontologies.genodexito.Genodexito method), [1] create_napistu_graph() (in module napistu.network.net_create) create_neighborhood_dict_entry() (in module napistu.network.neighborhoods) create_neighborhoods() (in module napistu.network.neighborhoods) create_package_importer() (in module napistu.utils.optional) create_parent_child_graph() (in module napistu.ingestion.obo) create_pathway_index_df() (in module napistu.indices) create_python_mapping_tables() (in module napistu.ontologies.mygene) create_reaction_formula_series() (in module napistu.sbml_dfs_utils) create_source_table() (in module napistu.source) create_species_df() (in module napistu.ingestion.reactome_fi) create_uri_url() (in module napistu.ontologies.standardization) CROSSREF_CSV napistu-refine-add_reactome_identifiers command line option curate_sbml_dfs() (in module napistu.modify.curation) CURATION_DIR napistu-refine-apply_manual_curations command line option custom_loaders (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) custom_urls (napistu.ingestion.harmonizome.HarmonizomeDataset attribute)

D

data (napistu.genomics.scverse_loading.DatasetsConfig attribute), [1] DatasetConfig (class in napistu.genomics.scverse_loading) DatasetsConfig (class in napistu.genomics.scverse_loading) dbver (napistu.genomics.gsea.GmtsConfig attribute) deduplicate_edges (napistu.network.ng_core.NapistuGraph attribute) deduplicate_edges() (napistu.network.ng_core.NapistuGraph method) define_graph_universe() (in module napistu.network.ig_utils) description (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) df (napistu.identifiers.Identifiers attribute) (napistu.network.edgelist.Edgelist attribute) df_to_identifiers() (in module napistu.identifiers) discretize_expression_data() (in module napistu.context.discretize) display() (in module napistu.sbml_dfs_utils) display_post_consensus_checks() (in module napistu.sbml_dfs_utils) DockerImageManager (class in napistu.utils.docker_utils) document (napistu.ingestion.sbml.SBML attribute) downcast_float_dataframe() (in module napistu.utils) (in module napistu.utils.pd_utils) download() (napistu.ingestion.harmonizome.HarmonizomeDataset method)

download_and_extract() (in module napistu.utils) (in module napistu.utils.io_utils) download_and_process() (napistu.ingestion.harmonizome.HarmonizomeDataset method) download_files (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) download_ftp() (in module napistu.utils) (in module napistu.utils.io_utils) download_go_basic_obo() (in module napistu.ingestion.obo) download_gtex_rnaseq() (in module napistu.ingestion.gtex) download_hpa_data() (in module napistu.ingestion.hpa) download_intact_xmls() (in module napistu.ingestion.intact) download_public_napistu_asset() (in module napistu.gcs.downloads) download_reactome_fi() (in module napistu.ingestion.reactome_fi) download_string() (in module napistu.ingestion.string) download_string_aliases() (in module napistu.ingestion.string) download_trrust() (in module napistu.ingestion.trrust) download_wget() (in module napistu.utils) (in module napistu.utils.io_utils) drop_cofactors() (in module napistu.modify.cofactors) drop_extra_cols() (in module napistu.utils) (in module napistu.utils.pd_utils)

E

Edgelist (class in napistu.network.edgelist) edgelist_ora() (in module napistu.genomics.gsea) edgelist_to_pathway_species() (in module napistu.matching.interactions) edgelist_to_scids() (in module napistu.matching.interactions) empty() (napistu.source.Source class method) engine (napistu.genomics.gsea.GmtsConfig attribute) ensembl_id_to_url_regex() (in module napistu.ontologies.standardization) ensure (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) ensure() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator class method) (napistu.network.edgelist.Edgelist class method) ensure_available (napistu.utils.docker_utils.DockerImageManager attribute) ensure_available() (napistu.utils.docker_utils.DockerImageManager method) ensure_harmonizome_dataset() (napistu.ingestion.harmonizome.HarmonizomeDataset class method) ensure_path() (in module napistu.utils.path_utils) ensure_pd_df() (in module napistu.utils) (in module napistu.utils.pd_utils)

ENTITY_SET_CSV napistu-refine-add_reactome_entity_sets command line option except_any (napistu.modify.cofactors.CofactorFilterRule attribute) expand_sbml_dfs_ids() (napistu.ontologies.genodexito.Genodexito method), [1] export_sbml_dfs (napistu.sbml_dfs_core.SBML_dfs attribute) export_sbml_dfs() (napistu.sbml_dfs_core.SBML_dfs method) extra_vars (napistu.utils.match_pd_vars attribute) (napistu.utils.pd_utils.match_pd_vars attribute) extract() (in module napistu.utils) (in module napistu.utils.io_utils) extract_regex_match() (in module napistu.utils) (in module napistu.utils.string_utils) extract_regex_search() (in module napistu.utils) (in module napistu.utils.string_utils)

F

features_to_pathway_species() (in module napistu.matching.species) file (napistu.gcs.assets.GCSAsset attribute) filter() (napistu.indices.PWIndex method), [1] filter_by_species_type() (napistu.network.ng_core.NapistuGraph method) filter_id_table() (in module napistu.ontologies.id_tables) filter_precomputed_distances_top_n() (in module napistu.network.precompute) filter_reactions_with_disconnected_cspecies() (in module napistu.context.filtering) filter_species_by_attribute() (in module napistu.context.filtering) filter_to_characteristic_species_ids() (in module napistu.sbml_dfs_utils) filter_to_direct_mechanistic_interactions() (in module napistu.matching.interactions) filter_to_indirect_mechanistic_interactions() (in module napistu.matching.interactions) filter_to_largest_subgraph() (in module napistu.network.ig_utils) filter_to_largest_subgraphs() (in module napistu.network.ig_utils) find_all_shortest_reaction_paths() (in module napistu.network.paths) find_and_prune_neighborhoods() (in module napistu.network.neighborhoods) find_entity_references (napistu.sbml_dfs_core.SBML_dfs attribute) find_entity_references() (napistu.sbml_dfs_core.SBML_dfs method) find_neighborhoods() (in module napistu.network.neighborhoods) find_peaks() (napistu.context.discretize.PeakSelector method) find_shortest_reaction_paths() (in module napistu.network.paths) find_species_with_attribute() (in module napistu.context.filtering) find_underspecified_reactions() (in module napistu.sbml_dfs_utils) find_unused_entities() (in module napistu.sbml_dfs_utils) find_weakly_connected_subgraphs() (in module napistu.utils) (in module napistu.utils.ig_utils) fisher_exact_vectorized() (in module napistu.statistics.hypothesis_testing) force_edgelist_consistency() (in module napistu.sbml_dfs_utils) format_curated_entities() (in module napistu.modify.curation)

format_curations() (in module napistu.modify.curation) format_identifiers_as_edgelist() (in module napistu.utils) (in module napistu.utils.pd_utils) format_napistu_graph_summary() (in module napistu.network.ng_utils) format_obo_dict_as_df() (in module napistu.ingestion.obo) format_omnipath_as_sbml_dfs() (in module napistu.ingestion.omnipath) format_psi_mi() (in module napistu.ingestion.psi_mi) format_psi_mis() (in module napistu.ingestion.psi_mi) format_sbml_dfs_summary() (in module napistu.sbml_dfs_utils) format_tiered_reaction_species() (in module napistu.network.net_create_utils) format_uri() (in module napistu.ontologies.standardization) format_uri_url() (in module napistu.ontologies.standardization) format_uri_url_identifiers_dot_org() (in module napistu.ontologies.standardization) from_dict() (napistu.gcs.assets.GCSAssets class method) (napistu.genomics.scverse_loading.MultiModalityOntologyConfig class method) (napistu.ingestion.harmonizome.HarmonizomeDataset class method) (napistu.ingestion.sbml.CompartmentAliasesValidator class method) from_edgelist (napistu.sbml_dfs_core.SBML_dfs attribute) from_edgelist() (napistu.sbml_dfs_core.SBML_dfs class method) from_igraph (napistu.network.ng_core.NapistuGraph attribute) from_igraph() (napistu.network.ng_core.NapistuGraph class method) from_pickle (napistu.network.ng_core.NapistuGraph attribute) (napistu.sbml_dfs_core.SBML_dfs attribute) from_pickle() (napistu.network.ng_core.NapistuGraph class method) (napistu.sbml_dfs_core.SBML_dfs class method) full_image_name (napistu.utils.docker_utils.DockerImageManager attribute) (napistu.utils.docker_utils.DockerImageManager property) full_name (napistu.utils.docker_utils.ImageInfo attribute) (napistu.utils.docker_utils.ImageInfo property)

G

GCSAsset (class in napistu.gcs.assets) GCSAssets (class in napistu.gcs.assets) generate_simple_test_data() (in module napistu.context.discretize) GenesetCollection (class in napistu.genomics.gsea) Genodexito (class in napistu.ontologies.genodexito) get (napistu.genomics.scverse_loading.DatasetsConfig attribute) get() (napistu.genomics.scverse_loading.DatasetsConfig method) get_all_bqbs (napistu.identifiers.Identifiers attribute) get_all_bqbs() (napistu.identifiers.Identifiers method) get_all_chebi_ids() (napistu.modify.cofactors.CofactorChebiIDs method) get_all_ontologies (napistu.identifiers.Identifiers attribute) get_all_ontologies() (napistu.identifiers.Identifiers method) get_available_species (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) get_available_species() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator class method) get_characteristic_species_ids (napistu.sbml_dfs_core.SBML_dfs attribute) get_characteristic_species_ids() (napistu.sbml_dfs_core.SBML_dfs method) get_chebi_to_cofactor_map() (napistu.modify.cofactors.CofactorChebiIDs method) get_cspecies_features (napistu.sbml_dfs_core.SBML_dfs attribute) get_cspecies_features() (napistu.sbml_dfs_core.SBML_dfs method) get_current_max_id() (in module napistu.sbml_dfs_utils) get_default_collection_config() (in module napistu.genomics.gsea) get_download_urls() (napistu.ingestion.harmonizome.HarmonizomeDataset method) get_edge_dataframe (napistu.network.ng_core.NapistuGraph attribute) get_edge_dataframe() (napistu.network.ng_core.NapistuGraph method) get_edge_endpoint_attributes() (napistu.network.ng_core.NapistuGraph method) get_edge_series (napistu.network.ng_core.NapistuGraph attribute) get_edge_series() (napistu.network.ng_core.NapistuGraph method) get_extn_from_url() (in module napistu.utils) (in module napistu.utils.path_utils) get_gmt_as_df (napistu.genomics.gsea.GenesetCollection attribute) get_gmt_as_df() (napistu.genomics.gsea.GenesetCollection method) get_gmt_w_napistu_ids() (napistu.genomics.gsea.GenesetCollection method) get_graph_summary() (in module napistu.network.ig_utils) get_has_reactions() (napistu.network.ng_core.NapistuGraph method) get_identifiers (napistu.sbml_dfs_core.SBML_dfs attribute) get_identifiers() (napistu.sbml_dfs_core.SBML_dfs method) get_interactions() (in module napistu.ingestion.omnipath) get_merge_keys() (in module napistu.network.ig_utils) get_metadata (napistu.network.ng_core.NapistuGraph attribute) get_metadata() (napistu.network.ng_core.NapistuGraph method) get_minimal_sources_edges() (in module napistu.network.ng_utils) get_napistu_r() (in module napistu.rpy2.callr) get_napistu_r_package() (in module napistu.rpy2) get_ontology_cooccurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_ontology_cooccurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_ontology_occurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_ontology_occurrence() (napistu.sbml_dfs_core.SBML_dfs method)

get_ontology_x_source_cooccurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_ontology_x_source_cooccurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_rbase() (in module napistu.rpy2.callr) get_rpy2_availability() (in module napistu.rpy2) get_rpy2_core_modules() (in module napistu.rpy2) get_rpy2_extended_modules() (in module napistu.rpy2) get_sbml_dfs_vertex_summaries() (in module napistu.network.ng_utils) get_sbo_term_occurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_sbo_term_occurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_sbo_term_x_source_cooccurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_sbo_term_x_source_cooccurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_source_base_and_path() (in module napistu.utils) (in module napistu.utils.path_utils) get_source_cooccurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_source_cooccurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_source_occurrence (napistu.sbml_dfs_core.SBML_dfs attribute) get_source_occurrence() (napistu.sbml_dfs_core.SBML_dfs method) get_source_total_counts (napistu.sbml_dfs_core.SBML_dfs attribute) get_source_total_counts() (napistu.sbml_dfs_core.SBML_dfs method) get_sources (napistu.sbml_dfs_core.SBML_dfs attribute) get_sources() (napistu.sbml_dfs_core.SBML_dfs method) get_species_features (napistu.sbml_dfs_core.SBML_dfs attribute) get_species_features() (napistu.sbml_dfs_core.SBML_dfs method) get_string_species_url() (in module napistu.ingestion.string) get_summary (napistu.sbml_dfs_core.SBML_dfs attribute) get_summary() (napistu.network.ng_core.NapistuGraph method) (napistu.sbml_dfs_core.SBML_dfs method) get_table (napistu.sbml_dfs_core.SBML_dfs attribute) get_table() (napistu.sbml_dfs_core.SBML_dfs method) get_target_base_and_path() (in module napistu.utils) (in module napistu.utils.path_utils) get_uri_urls (napistu.sbml_dfs_core.SBML_dfs attribute) get_uri_urls() (napistu.sbml_dfs_core.SBML_dfs method) get_vertex_dataframe (napistu.network.ng_core.NapistuGraph attribute) get_vertex_dataframe() (napistu.network.ng_core.NapistuGraph method) get_vertex_series (napistu.network.ng_core.NapistuGraph attribute) get_vertex_series() (napistu.network.ng_core.NapistuGraph method) gmt (napistu.genomics.gsea.GenesetCollection attribute) gmts (napistu.genomics.gsea.GenesetCollection attribute) GmtsConfig (class in napistu.genomics.gsea) graph_to_pandas_dfs() (in module napistu.network.ig_utils) GRAPH_URI napistu-exporter-export_precomputed_distances command line option GTEX_FILE_URI napistu-refine-filter_gtex_tissue command line option gunzip() (in module napistu.utils) (in module napistu.utils.io_utils)

H

HarmonizomeDataset (class in napistu.ingestion.harmonizome) has_duplicated_edges (napistu.network.edgelist.Edgelist property) has_ontology (napistu.identifiers.Identifiers attribute) has_ontology() (napistu.identifiers.Identifiers method)

has_reciprocal_edges (napistu.network.edgelist.Edgelist property) hoist (napistu.identifiers.Identifiers attribute) hoist() (napistu.identifiers.Identifiers method) HPA_FILE_URI napistu-refine-filter_hpa_compartments command line option

I

id_formatter() (in module napistu.sbml_dfs_utils) id_formatter_inv() (in module napistu.sbml_dfs_utils) id_list (napistu.identifiers._IdentifiersValidator attribute) identifier (napistu.identifiers._IdentifierValidator attribute) Identifiers (class in napistu.identifiers) identify_cofactors() (in module napistu.modify.cofactors) ids (napistu.identifiers.Identifiers attribute) (napistu.identifiers.Identifiers property) if_all (napistu.modify.cofactors.CofactorFilterRule attribute) image_info (napistu.utils.docker_utils.DockerImageManager attribute) ImageInfo (class in napistu.utils.docker_utils) import_anndata() (in module napistu.utils.optional) import_beautifulsoup() (in module napistu.utils.optional) import_gseapy() (in module napistu.utils.optional) import_libsbml() (in module napistu.utils.optional) import_mudata() (in module napistu.utils.optional) import_omnipath() (in module napistu.utils.optional) import_omnipath_interactions() (in module napistu.utils.optional) import_package() (in module napistu.utils.optional) import_statsmodels() (in module napistu.utils.optional) import_statsmodels_multitest() (in module napistu.utils.optional) index (napistu.indices.PWIndex attribute) index_which_ontology (napistu.genomics.scverse_loading.ModalityOntologyConfig attribute) infer_entity_type() (in module napistu.utils) (in module napistu.utils.pd_utils)

infer_sbo_terms (napistu.sbml_dfs_core.SBML_dfs attribute) infer_sbo_terms() (napistu.sbml_dfs_core.SBML_dfs method) infer_uncompartmentalized_species_location (napistu.sbml_dfs_core.SBML_dfs attribute) infer_uncompartmentalized_species_location() (napistu.sbml_dfs_core.SBML_dfs method) ingest_replogle_pvalues() (in module napistu.ingestion.perturbseq) initialize_dir() (in module napistu.utils) (in module napistu.utils.path_utils) INPUT_URI napistu-helpers-copy_uri command line option napistu-importer-sbml command line option napistu-importer-sbml_dfs command line option napistu-stats-igraph_network command line option intact_to_sbml_dfs() (in module napistu.ingestion.intact) INTACT_XML_DIR napistu-integrate-intact command line option is_available (napistu.utils.docker_utils.DockerImageManager attribute) is_available() (napistu.utils.docker_utils.DockerImageManager method) is_known_unsupported_uri() (in module napistu.ontologies.standardization) is_local (napistu.utils.docker_utils.ImageInfo attribute) (napistu.utils.docker_utils.ImageInfo property) is_reversed (napistu.network.ng_core.NapistuGraph attribute) (napistu.network.ng_core.NapistuGraph property) items (napistu.genomics.scverse_loading.DatasetsConfig attribute) items() (napistu.genomics.scverse_loading.DatasetsConfig method) (napistu.genomics.scverse_loading.MultiModalityOntologyConfig method) (napistu.ingestion.sbml.CompartmentAliasesValidator method)

K

keys (napistu.genomics.scverse_loading.DatasetsConfig attribute)

keys() (napistu.genomics.scverse_loading.DatasetsConfig method)

L

latin_name (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) (napistu.ingestion.organismal_species.OrganismalSpeciesValidator property) load() (napistu.ingestion.harmonizome.HarmonizomeDataset method) load_and_clean_gtex_data() (in module napistu.ingestion.gtex) load_and_clean_hpa_data() (in module napistu.ingestion.hpa) load_h5ad (napistu.genomics.scverse_loading.DatasetConfig attribute) load_h5ad() (napistu.genomics.scverse_loading.DatasetConfig method) load_h5mu (napistu.genomics.scverse_loading.DatasetConfig attribute) load_h5mu() (napistu.genomics.scverse_loading.DatasetConfig method) load_harmonizome_datasets() (in module napistu.ingestion.harmonizome) load_harmonizome_perturbseq_datasets() (in module napistu.ingestion.perturbseq)

load_json() (in module napistu.utils) (in module napistu.utils.io_utils) load_mirbase_table() (in module napistu.ontologies.mirbase) load_mirbase_xrefs() (in module napistu.ontologies.mirbase) load_parquet() (in module napistu.utils) (in module napistu.utils.io_utils) load_pickle() (in module napistu.utils) (in module napistu.utils.io_utils) load_public_napistu_asset() (in module napistu.gcs.downloads) load_replogle_pvalues_with_species_ids() (in module napistu.ingestion.perturbseq) lookup_custom_value (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) lookup_custom_value() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator method)

M

major (napistu.context.discretize.PeakIndices attribute) map_pubchem_ids() (in module napistu.ontologies.pubchem) mapper_used (napistu.ontologies.genodexito.Genodexito attribute) mappings (napistu.ontologies.genodexito.Genodexito attribute) match_by_ontology_and_identifier() (in module napistu.matching.species) match_entitydata_index_to_entity() (in module napistu.sbml_dfs_utils) match_features_to_wide_pathway_species() (in module napistu.matching.species) match_pd_vars (class in napistu.utils) (class in napistu.utils.pd_utils) match_regex_dict() (in module napistu.utils) (in module napistu.utils.string_utils) matrix_to_edgelist() (in module napistu.utils) (in module napistu.utils.pd_utils) melt_propagation_results() (in module napistu.network.net_propagation) merge() (napistu.identifiers.Identifiers class method) merge_edgelists() (napistu.network.edgelist.Edgelist method) merge_mappings() (napistu.ontologies.genodexito.Genodexito method), [1] merge_sources() (in module napistu.source) merged_mappings (napistu.ontologies.genodexito.Genodexito attribute) method (napistu.network.net_propagation.PropagationMethod attribute) minor (napistu.context.discretize.PeakIndices attribute) missing_vars (napistu.utils.match_pd_vars attribute) (napistu.utils.pd_utils.match_pd_vars attribute) ModalityOntologyConfig (class in napistu.genomics.scverse_loading) model (napistu.ingestion.sbml.SBML attribute) model_config (napistu.gcs.assets.GCSAsset attribute) (napistu.gcs.assets.GCSAssets attribute) (napistu.genomics.gsea.GmtsConfig attribute) (napistu.genomics.scverse_loading.DatasetConfig attribute) (napistu.genomics.scverse_loading.ModalityOntologyConfig attribute) (napistu.genomics.scverse_loading.MultiModalityOntologyConfig attribute) (napistu.identifiers._IdentifiersValidator attribute) (napistu.identifiers._IdentifierValidator attribute) (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) (napistu.ingestion.sbml.CompartmentAliasesValidator attribute) (napistu.modify.cofactors.CofactorChebiIDs attribute) (napistu.modify.cofactors.CofactorFilterRule attribute) (napistu.modify.cofactors.CofactorSchema attribute) (napistu.network.ng_utils._EntityAttrValidator attribute) (napistu.utils.docker_utils.ImageInfo attribute) module napistu napistu.consensus napistu.constants napistu.context napistu.context.discretize napistu.context.filtering napistu.gcs napistu.gcs.assets napistu.gcs.constants napistu.gcs.downloads napistu.gcs.utils napistu.genomics napistu.genomics.constants napistu.genomics.gsea napistu.genomics.scverse_loading napistu.identifiers napistu.indices napistu.ingestion napistu.ingestion.bigg napistu.ingestion.constants napistu.ingestion.gtex napistu.ingestion.harmonizome napistu.ingestion.hpa napistu.ingestion.identifiers_etl napistu.ingestion.intact napistu.ingestion.napistu_edgelist napistu.ingestion.obo napistu.ingestion.omnipath napistu.ingestion.organismal_species napistu.ingestion.perturbseq napistu.ingestion.psi_mi napistu.ingestion.reactome napistu.ingestion.reactome_fi napistu.ingestion.sbml napistu.ingestion.string napistu.ingestion.trrust napistu.matching napistu.matching.constants napistu.matching.interactions napistu.matching.mount napistu.matching.species napistu.modify napistu.modify.cofactors napistu.modify.constants napistu.modify.curation napistu.modify.gaps napistu.modify.pathwayannot napistu.modify.uncompartmentalize napistu.network napistu.network.clustering napistu.network.constants napistu.network.data_handling napistu.network.edgelist napistu.network.ig_utils napistu.network.neighborhoods napistu.network.net_create napistu.network.net_create_utils napistu.network.net_propagation napistu.network.ng_core napistu.network.ng_utils napistu.network.paths napistu.network.precompute napistu.ontologies napistu.ontologies.constants napistu.ontologies.dogma napistu.ontologies.genodexito napistu.ontologies.id_tables napistu.ontologies.mirbase napistu.ontologies.mygene napistu.ontologies.pubchem napistu.ontologies.renaming napistu.ontologies.standardization napistu.rpy2 napistu.rpy2.callr napistu.rpy2.constants napistu.rpy2.rids napistu.sbml_dfs_core napistu.sbml_dfs_utils napistu.source napistu.statistics napistu.statistics.constants napistu.statistics.hypothesis_testing napistu.statistics.quantiles napistu.utils napistu.utils.constants napistu.utils.display_utils napistu.utils.docker_utils napistu.utils.ig_utils napistu.utils.io_utils napistu.utils.optional napistu.utils.path_utils napistu.utils.pd_utils napistu.utils.string_utils

MultiModalityOntologyConfig (class in napistu.genomics.scverse_loading)

N

name (napistu.genomics.scverse_loading.DatasetConfig attribute), [1] (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) (napistu.utils.docker_utils.ImageInfo attribute), [1] name_compartmentalized_species (napistu.sbml_dfs_core.SBML_dfs attribute) name_compartmentalized_species() (napistu.sbml_dfs_core.SBML_dfs method) napistu module napistu-consensus-check command line option --verbosity -v SBML_DFS_URI napistu-consensus-create command line option --ignore-mergeability --nondogmatic --verbosity -n -v OUTPUT_MODEL_URI SBML_DFS_URIS napistu-exporter-export_napistu_graph command line option --deduplicate_edges --directed --drop_reactions_when --format --graph_attrs_spec_uri --reverse --weighting_strategy --wiring_approach -a -d -f -g -r -w -x OUTPUT_URI SBML_DFS_URI napistu-exporter-export_precomputed_distances command line option --format --max_score_q --max_steps --partition_size --weight_vars -f -p -q -s -w GRAPH_URI OUTPUT_URI napistu-exporter-export_smbl_dfs_tables command line option --model-prefix --nondogmatic --overwrite --verbosity -m -n -v OUTPUT_URI SBML_DFS_URI napistu-helpers-copy_uri command line option --is-file --verbosity -v INPUT_URI OUTPUT_URI napistu-helpers-summarize_sbml_dfs command line option --verbosity -v SBML_DFS_URI napistu-helpers-validate_assets command line option --identifiers_df_uri --napistu_graph_uri --precomputed_distances_uri --verbosity -d -g -i -v SBML_DFS_URI napistu-helpers-validate_sbml_dfs command line option --verbosity -v SBML_DFS_URI napistu-importer-sbml command line option --verbosity -v INPUT_URI OUTPUT_MODEL_URI napistu-importer-sbml_dfs command line option --verbosity -v INPUT_URI OUTPUT_MODEL_URI SBML_DFS_URI napistu-ingestion-bigg command line option --overwrite --verbosity -v BASE_FOLDER napistu-ingestion-gtex-rnaseq-expression command line option --url --verbosity -v TARGET_URI napistu-ingestion-intact command line option --overwrite --verbosity -v ORGANISMAL_SPECIES OUTPUT_DIR_PATH napistu-ingestion-proteinatlas_subcell command line option --url --verbosity -v TARGET_URI napistu-ingestion-reactome command line option --overwrite --verbosity -v BASE_FOLDER napistu-ingestion-reactome_fi command line option --overwrite --url --verbosity -v TARGET_URI napistu-ingestion-string_aliases command line option --verbosity -v ORGANISMAL_SPECIES TARGET_URI napistu-ingestion-string_db command line option --verbosity -v ORGANISMAL_SPECIES TARGET_URI napistu-ingestion-trrust command line option --verbosity -v TARGET_URI napistu-integrate-bigg command line option --overwrite --verbosity -v ORGANISMAL_SPECIES OUTPUT_MODEL_URI PW_INDEX_URI napistu-integrate-dogmatic_scaffold command line option --allow-fallback --preferred-method --verbosity -a -p -v ORGANISMAL_SPECIES OUTPUT_MODEL_URI napistu-integrate-intact command line option --overwrite --verbosity -v INTACT_XML_DIR ORGANISMAL_SPECIES OUTPUT_MODEL_URI napistu-integrate-omnipath command line option --allow-fallback --overwrite --preferred-method --verbosity -a -p -v ORGANISMAL_SPECIES OUTPUT_MODEL_URI napistu-integrate-reactome command line option --overwrite --permissive --verbose --verbosity -p -v, [1] ORGANISMAL_SPECIES OUTPUT_MODEL_URI PW_INDEX_URI napistu-integrate-reactome_fi command line option --allow-fallback --overwrite --preferred-method --verbosity -a -p -v OUTPUT_MODEL_URI REACTOME_FI_URI napistu-integrate-string_db command line option --overwrite --verbosity -v ORGANISMAL_SPECIES OUTPUT_MODEL_URI STRING_ALIASES_URI STRING_DB_URI napistu-integrate-trrust command line option --overwrite --verbosity -v OUTPUT_MODEL_URI TRRUST_CSV_URI napistu-refine-add_reactome_entity_sets command line option ENTITY_SET_CSV OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-add_reactome_identifiers command line option CROSSREF_CSV OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-add_transportation_reactions command line option --exchange-compartment --verbosity -e -v OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-apply_manual_curations command line option CURATION_DIR OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-drop_cofactors command line option OUTPUT_MODEL_URI SBML_DFS_URI

napistu-refine-expand_identifiers command line option --allow-fallback --ontologies --preferred-method -a -o -p ORGANISMAL_SPECIES OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-filter_gtex_tissue command line option --verbosity -v GTEX_FILE_URI OUTPUT_MODEL_URI SBML_DFS_URI TISSUE napistu-refine-filter_hpa_compartments command line option --verbosity -v HPA_FILE_URI OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-infer_uncompartmentalized_species_location command line option OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-merge_model_compartments command line option OUTPUT_MODEL_URI SBML_DFS_URI napistu-refine-name_compartmentalized_species command line option OUTPUT_MODEL_URI SBML_DFS_URI napistu-stats-igraph_network command line option INPUT_URI OUTPUT_URI napistu-stats-sbml_dfs_network command line option OUTPUT_URI SBML_DFS_URI napistu.consensus module napistu.constants module napistu.context module napistu.context.discretize module napistu.context.filtering module napistu.gcs module napistu.gcs.assets module napistu.gcs.constants module napistu.gcs.downloads module napistu.gcs.utils module napistu.genomics module napistu.genomics.constants module napistu.genomics.gsea module napistu.genomics.scverse_loading module napistu.identifiers module napistu.indices module napistu.ingestion module napistu.ingestion.bigg module napistu.ingestion.constants module napistu.ingestion.gtex module napistu.ingestion.harmonizome module napistu.ingestion.hpa module napistu.ingestion.identifiers_etl module napistu.ingestion.intact module napistu.ingestion.napistu_edgelist module napistu.ingestion.obo module napistu.ingestion.omnipath module napistu.ingestion.organismal_species module napistu.ingestion.perturbseq module napistu.ingestion.psi_mi module napistu.ingestion.reactome module napistu.ingestion.reactome_fi module napistu.ingestion.sbml module napistu.ingestion.string module napistu.ingestion.trrust module napistu.matching module napistu.matching.constants module napistu.matching.interactions module napistu.matching.mount module napistu.matching.species module napistu.modify module napistu.modify.cofactors module napistu.modify.constants module napistu.modify.curation module napistu.modify.gaps module napistu.modify.pathwayannot module napistu.modify.uncompartmentalize module napistu.network module napistu.network.clustering module napistu.network.constants module napistu.network.data_handling module napistu.network.edgelist module napistu.network.ig_utils module napistu.network.neighborhoods module napistu.network.net_create module napistu.network.net_create_utils module napistu.network.net_propagation module napistu.network.ng_core module napistu.network.ng_utils module napistu.network.paths module napistu.network.precompute module napistu.ontologies module napistu.ontologies.constants module napistu.ontologies.dogma module napistu.ontologies.genodexito module napistu.ontologies.id_tables module napistu.ontologies.mirbase module napistu.ontologies.mygene module napistu.ontologies.pubchem module napistu.ontologies.renaming module napistu.ontologies.standardization module napistu.rpy2 module napistu.rpy2.callr module napistu.rpy2.constants module napistu.rpy2.rids module napistu.sbml_dfs_core module napistu.sbml_dfs_utils module napistu.source module napistu.statistics module napistu.statistics.constants module napistu.statistics.hypothesis_testing module napistu.statistics.quantiles module napistu.utils module napistu.utils.constants module napistu.utils.display_utils module napistu.utils.docker_utils module napistu.utils.ig_utils module napistu.utils.io_utils module napistu.utils.optional module napistu.utils.path_utils module napistu.utils.pd_utils module napistu.utils.string_utils module NapistuGraph (class in napistu.network.ng_core) net_propagate_attributes() (in module napistu.network.net_propagation) network_propagation_with_null() (in module napistu.network.net_propagation) network_propagation_with_null_repeated() (in module napistu.network.net_propagation) non_negative (napistu.network.net_propagation.PropagationMethod attribute)

O

ontologies (napistu.genomics.scverse_loading.ModalityOntologyConfig attribute) ontology (napistu.identifiers._IdentifierValidator attribute) ORGANISMAL_SPECIES napistu-ingestion-intact command line option napistu-ingestion-string_aliases command line option napistu-ingestion-string_db command line option napistu-integrate-bigg command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-intact command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option napistu-integrate-string_db command line option napistu-refine-expand_identifiers command line option organismal_species (napistu.genomics.gsea.GenesetCollection attribute) OrganismalSpeciesValidator (class in napistu.ingestion.organismal_species) other (napistu.context.discretize.PeakIndices attribute) OUTPUT_DIR_PATH napistu-ingestion-intact command line option OUTPUT_MODEL_URI napistu-consensus-create command line option napistu-importer-sbml command line option napistu-importer-sbml_dfs command line option napistu-integrate-bigg command line option napistu-integrate-dogmatic_scaffold command line option napistu-integrate-intact command line option napistu-integrate-omnipath command line option napistu-integrate-reactome command line option napistu-integrate-reactome_fi command line option napistu-integrate-string_db command line option napistu-integrate-trrust command line option napistu-refine-add_reactome_entity_sets command line option napistu-refine-add_reactome_identifiers command line option napistu-refine-add_transportation_reactions command line option napistu-refine-apply_manual_curations command line option napistu-refine-drop_cofactors command line option napistu-refine-expand_identifiers command line option napistu-refine-filter_gtex_tissue command line option napistu-refine-filter_hpa_compartments command line option napistu-refine-infer_uncompartmentalized_species_location command line option napistu-refine-merge_model_compartments command line option napistu-refine-name_compartmentalized_species command line option

OUTPUT_URI napistu-exporter-export_napistu_graph command line option napistu-exporter-export_precomputed_distances command line option napistu-exporter-export_smbl_dfs_tables command line option napistu-helpers-copy_uri command line option napistu-stats-igraph_network command line option napistu-stats-sbml_dfs_network command line option

P

pandas_to_r_dataframe() (in module napistu.rpy2.callr) parse_ensembl_id() (in module napistu.ontologies.standardization) path (napistu.genomics.scverse_loading.DatasetConfig attribute), [1] path_exists() (in module napistu.utils) (in module napistu.utils.path_utils) PeakIndices (class in napistu.context.discretize) PeakSelector (class in napistu.context.discretize) pickle_cache() (in module napistu.utils) (in module napistu.utils.io_utils) platform (napistu.utils.docker_utils.ImageInfo attribute), [1] plot_neighborhood() (in module napistu.network.neighborhoods) plot_shortest_paths() (in module napistu.network.paths) pluck_data() (in module napistu.network.ng_utils) pluck_entity_data() (in module napistu.network.ng_utils) post_consensus_checks (napistu.sbml_dfs_core.SBML_dfs attribute) post_consensus_checks() (napistu.sbml_dfs_core.SBML_dfs method) precompute_distances() (in module napistu.network.precompute) prepare_anndata_results_df() (in module napistu.genomics.scverse_loading) prepare_consensus_model() (in module napistu.consensus) prepare_entity_data_extraction() (in module napistu.network.ng_utils) prepare_mudata_results_df() (in module napistu.genomics.scverse_loading) print (napistu.identifiers.Identifiers attribute)

print() (napistu.identifiers.Identifiers method) process_edge_list() (napistu.ingestion.harmonizome.HarmonizomeDataset method) process_harmonizome_datasets() (in module napistu.ingestion.harmonizome) process_napistu_graph() (in module napistu.network.net_create) project (napistu.gcs.assets.GCSAssets attribute) PropagationMethod (class in napistu.network.net_propagation) Properties (napistu.identifiers.Identifiers attribute) (napistu.network.edgelist.Edgelist attribute) (napistu.utils.docker_utils.DockerImageManager attribute) (napistu.utils.docker_utils.ImageInfo attribute) proportion_test_vectorized() (in module napistu.statistics.hypothesis_testing) prune_neighborhoods() (in module napistu.network.neighborhoods) PubChemConnectivityError public_url (napistu.gcs.assets.GCSAsset attribute) pull (napistu.utils.docker_utils.DockerImageManager attribute) pull() (napistu.utils.docker_utils.DockerImageManager method) pull_name (napistu.utils.docker_utils.ImageInfo attribute) (napistu.utils.docker_utils.ImageInfo property) PW_INDEX_URI napistu-integrate-bigg command line option napistu-integrate-reactome command line option PWIndex (class in napistu.indices)

R

r_dataframe_to_pandas() (in module napistu.rpy2.callr) reaction_dict (napistu.ingestion.sbml.SBML_reaction attribute) reaction_formulas (napistu.sbml_dfs_core.SBML_dfs attribute) reaction_formulas() (napistu.sbml_dfs_core.SBML_dfs method) reaction_species (napistu.sbml_dfs_core.SBML_dfs attribute), [1] reaction_summaries (napistu.sbml_dfs_core.SBML_dfs attribute) reaction_summaries() (napistu.sbml_dfs_core.SBML_dfs method) reactions (napistu.sbml_dfs_core.SBML_dfs attribute), [1] reactions_data (napistu.sbml_dfs_core.SBML_dfs attribute), [1] REACTOME_FI_URI napistu-integrate-reactome_fi command line option reactome_sbml_download() (in module napistu.ingestion.reactome) read_graph_attrs_spec() (in module napistu.network.ng_utils) read_obo_as_dict() (in module napistu.ingestion.obo) read_pathway_curations() (in module napistu.modify.curation) read_sbo_ontology() (in module napistu.ingestion.identifiers_etl) read_yeast_identifiers() (in module napistu.ingestion.identifiers_etl) registry (napistu.utils.docker_utils.ImageInfo attribute), [1] remove_attributes (napistu.network.ng_core.NapistuGraph attribute) remove_attributes() (napistu.network.ng_core.NapistuGraph method) remove_duplicated_edges() (napistu.network.edgelist.Edgelist method) remove_entities (napistu.sbml_dfs_core.SBML_dfs attribute) remove_entities() (napistu.sbml_dfs_core.SBML_dfs method) remove_isolated_vertices (napistu.network.ng_core.NapistuGraph attribute) remove_isolated_vertices() (napistu.network.ng_core.NapistuGraph method) remove_reactions_data (napistu.sbml_dfs_core.SBML_dfs attribute) remove_reactions_data() (napistu.sbml_dfs_core.SBML_dfs method) remove_reciprocal_edges() (napistu.network.edgelist.Edgelist method)

remove_reciprocal_interactions() (in module napistu.ingestion.napistu_edgelist) remove_species_data (napistu.sbml_dfs_core.SBML_dfs attribute) remove_species_data() (napistu.sbml_dfs_core.SBML_dfs method) remove_unused (napistu.sbml_dfs_core.SBML_dfs attribute) remove_unused() (napistu.sbml_dfs_core.SBML_dfs method) rename_species_ontologies() (in module napistu.ontologies.renaming) report_r_exceptions() (in module napistu.rpy2) req_vars (napistu.utils.match_pd_vars attribute) (napistu.utils.pd_utils.match_pd_vars attribute) requests_retry_session() (in module napistu.utils) (in module napistu.utils.io_utils) require_anndata() (in module napistu.utils.optional) require_beautifulsoup() (in module napistu.utils.optional) require_gseapy() (in module napistu.utils.optional) require_libsbml() (in module napistu.utils.optional) require_mudata() (in module napistu.utils.optional) require_omnipath() (in module napistu.utils.optional) require_package() (in module napistu.utils.optional) require_rpy2() (in module napistu.rpy2) require_statsmodels() (in module napistu.utils.optional) resolve_matches() (in module napistu.matching.mount) reverse_edges (napistu.network.ng_core.NapistuGraph attribute) reverse_edges() (napistu.network.ng_core.NapistuGraph method) root (napistu.genomics.scverse_loading.MultiModalityOntologyConfig attribute) (napistu.ingestion.sbml.CompartmentAliasesValidator attribute), [1] rsession_info() (in module napistu.rpy2) run_command() (napistu.utils.docker_utils.DockerImageManager method) run_infomap() (in module napistu.network.clustering)

S

safe_capitalize() (in module napistu.utils) (in module napistu.utils.string_utils) safe_fill() (in module napistu.utils) (in module napistu.utils.string_utils) safe_join_set() (in module napistu.utils) (in module napistu.utils.string_utils) safe_series_tolist() (in module napistu.utils.pd_utils) save_json() (in module napistu.utils) (in module napistu.utils.io_utils) save_parquet() (in module napistu.utils) (in module napistu.utils.io_utils) save_pickle() (in module napistu.utils) (in module napistu.utils.io_utils) SBML (class in napistu.ingestion.sbml) SBML_dfs (class in napistu.sbml_dfs_core) sbml_dfs_from_sbml() (in module napistu.ingestion.sbml) SBML_DFS_URI napistu-consensus-check command line option napistu-exporter-export_napistu_graph command line option napistu-exporter-export_smbl_dfs_tables command line option napistu-helpers-summarize_sbml_dfs command line option napistu-helpers-validate_assets command line option napistu-helpers-validate_sbml_dfs command line option napistu-importer-sbml_dfs command line option napistu-refine-add_reactome_entity_sets command line option napistu-refine-add_reactome_identifiers command line option napistu-refine-add_transportation_reactions command line option napistu-refine-apply_manual_curations command line option napistu-refine-drop_cofactors command line option napistu-refine-expand_identifiers command line option napistu-refine-filter_gtex_tissue command line option napistu-refine-filter_hpa_compartments command line option napistu-refine-infer_uncompartmentalized_species_location command line option napistu-refine-merge_model_compartments command line option napistu-refine-name_compartmentalized_species command line option napistu-stats-sbml_dfs_network command line option SBML_DFS_URIS napistu-consensus-create command line option sbml_errors() (napistu.ingestion.sbml.SBML method), [1] SBML_reaction (class in napistu.ingestion.sbml) schema (napistu.sbml_dfs_core.SBML_dfs attribute), [1] schema_mapping (napistu.modify.cofactors.CofactorSchema attribute) score_nameness() (in module napistu.utils) (in module napistu.utils.string_utils)

search() (napistu.indices.PWIndex method), [1] search_by_ids (napistu.sbml_dfs_core.SBML_dfs attribute) search_by_ids() (napistu.sbml_dfs_core.SBML_dfs method) search_by_name (napistu.sbml_dfs_core.SBML_dfs attribute) search_by_name() (napistu.sbml_dfs_core.SBML_dfs method) select_species_data (napistu.sbml_dfs_core.SBML_dfs attribute) select_species_data() (napistu.sbml_dfs_core.SBML_dfs method) separate_entity_attrs_by_source() (in module napistu.network.ng_utils) series_to_none_filled_list() (in module napistu.utils.pd_utils) set_graph_attrs (napistu.network.ng_core.NapistuGraph attribute) set_graph_attrs() (napistu.network.ng_core.NapistuGraph method) set_metadata (napistu.network.ng_core.NapistuGraph attribute) set_metadata() (napistu.network.ng_core.NapistuGraph method) set_weights (napistu.network.ng_core.NapistuGraph attribute) set_weights() (napistu.network.ng_core.NapistuGraph method) short_name (napistu.ingestion.harmonizome.HarmonizomeDataset attribute) show() (in module napistu.utils) (in module napistu.utils.display_utils) show_summary (napistu.sbml_dfs_core.SBML_dfs attribute) show_summary() (napistu.network.ng_core.NapistuGraph method) (napistu.sbml_dfs_core.SBML_dfs method) single_entry() (napistu.source.Source class method) Source (class in napistu.source) source (napistu.source.Source attribute) source_col (napistu.network.edgelist.Edgelist attribute) source_set_coverage() (in module napistu.source) species (napistu.ingestion.sbml.SBML_reaction attribute) (napistu.sbml_dfs_core.SBML_dfs attribute), [1] species_data (napistu.sbml_dfs_core.SBML_dfs attribute), [1] species_status (napistu.sbml_dfs_core.SBML_dfs attribute) species_status() (napistu.sbml_dfs_core.SBML_dfs method) species_type_types() (in module napistu.sbml_dfs_utils) stack_mappings() (napistu.ontologies.genodexito.Genodexito method), [1] stacked_mappings (napistu.ontologies.genodexito.Genodexito attribute) standard_merge_by (napistu.network.edgelist.Edgelist attribute) (napistu.network.edgelist.Edgelist property) STRING_ALIASES_URI napistu-integrate-string_db command line option STRING_DB_URI napistu-integrate-string_db command line option stub_compartments() (in module napistu.sbml_dfs_utils) style_df() (in module napistu.utils) (in module napistu.utils.pd_utils) subassets (napistu.gcs.assets.GCSAsset attribute) summary() (napistu.ingestion.sbml.SBML method), [1]

T

table (napistu.network.ng_utils._EntityAttrValidator attribute) tag (napistu.utils.docker_utils.ImageInfo attribute), [1] target_col (napistu.network.edgelist.Edgelist attribute) TARGET_URI napistu-ingestion-gtex-rnaseq-expression command line option napistu-ingestion-proteinatlas_subcell command line option napistu-ingestion-reactome_fi command line option napistu-ingestion-string_aliases command line option napistu-ingestion-string_db command line option napistu-ingestion-trrust command line option TISSUE napistu-refine-filter_gtex_tissue command line option to_dataframe (napistu.network.edgelist.Edgelist attribute) to_dataframe() (napistu.network.edgelist.Edgelist method)

to_dict (napistu.sbml_dfs_core.SBML_dfs attribute) to_dict() (napistu.sbml_dfs_core.SBML_dfs method) to_pandas_dfs (napistu.network.ng_core.NapistuGraph attribute) to_pandas_dfs() (napistu.network.ng_core.NapistuGraph method) to_pickle (napistu.network.ng_core.NapistuGraph attribute) (napistu.sbml_dfs_core.SBML_dfs attribute) to_pickle() (napistu.network.ng_core.NapistuGraph method) (napistu.sbml_dfs_core.SBML_dfs method) trans (napistu.network.ng_utils._EntityAttrValidator attribute) transform_edges (napistu.network.ng_core.NapistuGraph attribute) transform_edges() (napistu.network.ng_core.NapistuGraph method) transform_vertices (napistu.network.ng_core.NapistuGraph attribute) transform_vertices() (napistu.network.ng_core.NapistuGraph method) TRRUST_CSV_URI napistu-integrate-trrust command line option

U

uncompartmentalize_sbml_dfs() (in module napistu.modify.uncompartmentalize) unnest_identifiers() (in module napistu.sbml_dfs_utils) unnest_mygene_ontology() (in module napistu.ontologies.mygene) unnest_sources() (in module napistu.source)

update_pathological_names() (in module napistu.utils) (in module napistu.utils.pd_utils) update_sbml_df_with_exchange() (in module napistu.modify.gaps) uri (napistu.genomics.scverse_loading.DatasetConfig attribute), [1] url (napistu.identifiers._IdentifierValidator attribute)

V

validate (napistu.network.ng_core.NapistuGraph attribute) (napistu.sbml_dfs_core.SBML_dfs attribute) validate() (napistu.network.ng_core.NapistuGraph method) (napistu.sbml_dfs_core.SBML_dfs method) validate_against_supported (napistu.ingestion.organismal_species.OrganismalSpeciesValidator attribute) validate_against_supported() (napistu.ingestion.organismal_species.OrganismalSpeciesValidator method) validate_aliases() (napistu.ingestion.sbml.CompartmentAliasesValidator class method) validate_and_resolve (napistu.sbml_dfs_core.SBML_dfs attribute) validate_and_resolve() (napistu.sbml_dfs_core.SBML_dfs method) validate_assets() (in module napistu.network.ng_utils) (napistu.gcs.assets.GCSAssets class method) validate_cofactor_chebi_structure() (napistu.modify.cofactors.CofactorChebiIDs class method) validate_cofactor_names() (napistu.modify.cofactors.CofactorFilterRule class method) validate_download_files() (napistu.ingestion.harmonizome.HarmonizomeDataset class method) validate_edge_attributes() (in module napistu.network.ig_utils) validate_if_all_not_empty() (napistu.modify.cofactors.CofactorFilterRule class method)

validate_merge() (in module napistu.utils.pd_utils) validate_path() (napistu.genomics.scverse_loading.DatasetConfig class method) validate_public_url() (napistu.gcs.assets.GCSAsset class method) validate_sbml_dfs_table() (in module napistu.sbml_dfs_utils) validate_schema_not_empty() (napistu.modify.cofactors.CofactorSchema class method) validate_single_source() (napistu.source.Source method) validate_subset() (napistu.network.edgelist.Edgelist method) validate_uri() (napistu.genomics.scverse_loading.DatasetConfig class method) validate_versions() (napistu.gcs.assets.GCSAsset class method) validate_vertex_attributes() (in module napistu.network.ig_utils) values (napistu.genomics.scverse_loading.DatasetsConfig attribute) values() (napistu.genomics.scverse_loading.DatasetsConfig method) variable (napistu.network.ng_utils._EntityAttrValidator attribute) verbose (napistu.ingestion.sbml.SBML attribute) versions (napistu.gcs.assets.GCSAsset attribute) vertex_ora() (in module napistu.genomics.gsea)

W

weight_by (napistu.network.ng_core.NapistuGraph attribute) (napistu.network.ng_core.NapistuGraph property) weighting_strategy (napistu.network.ng_core.NapistuGraph attribute) (napistu.network.ng_core.NapistuGraph property)

wire_reaction_species() (in module napistu.network.net_create_utils) wiring_approach (napistu.network.ng_core.NapistuGraph attribute) (napistu.network.ng_core.NapistuGraph property) write_file_contents_to_path() (in module napistu.utils) (in module napistu.utils.io_utils)

Z

zfpkm() (in module napistu.context.discretize)