Index A | B | C | D | F | G | H | I | L | M | N | O | P | R | S | T | U | V | W A add() (mosaicmpi.biomart.BiomartAttributePage method) add_cnmf_results() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) add_community_weights_to_graph() (mosaicmpi.Network method) (mosaicmpi.network.Network method) add_missing_community_colors() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) add_missing_dataset_colors() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) add_missing_metadata_colors() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) annotated_heatmap() (in module mosaicmpi.plots) append_to_history() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) assert_alive() (mosaicmpi.biomart.BiomartServer method) attribute_pages (mosaicmpi.biomart.BiomartDataset property) attributes (mosaicmpi.biomart.BiomartDataset property) B BiomartAttribute (class in mosaicmpi.biomart) BiomartAttributePage (class in mosaicmpi.biomart) BiomartDatabase (class in mosaicmpi.biomart) BiomartDataset (class in mosaicmpi.biomart) BiomartFilter (class in mosaicmpi.biomart) BiomartServer (class in mosaicmpi.biomart) C calculate() (mosaicmpi.nancorrmp.NaNCorrMp static method) calculate_cnmf_prediction_error() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) calculate_with_p_value() (mosaicmpi.nancorrmp.NaNCorrMp static method) cNMF (class in mosaicmpi.cnmf) Colors (class in mosaicmpi) (class in mosaicmpi.colors) combine_nmf() (mosaicmpi.cnmf.cNMF method) community_search() (mosaicmpi.Network method) (mosaicmpi.network.Network method) compare_community_jaccard_similarity() (in module mosaicmpi.network) compute_community_network_layout() (mosaicmpi.Network method) (mosaicmpi.network.Network method) compute_corr() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) compute_layout() (mosaicmpi.Network method) (mosaicmpi.network.Network method) compute_pairwise_thresholds() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) Config (class in mosaicmpi.config) consensus() (mosaicmpi.cnmf.cNMF method) (mosaicmpi.Network method) (mosaicmpi.network.Network method) count() (mosaicmpi.biomart.BiomartDataset method) count_intracommunity_edges() (mosaicmpi.Network method) (mosaicmpi.network.Network method) create_community_network() (mosaicmpi.Network method) (mosaicmpi.network.Network method) create_program_network() (mosaicmpi.Network method) (mosaicmpi.network.Network method) cross_validate_imputation() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) D databases (mosaicmpi.biomart.BiomartServer property) Dataset (class in mosaicmpi) (class in mosaicmpi.dataset) datasets (mosaicmpi.biomart.BiomartDatabase property) (mosaicmpi.biomart.BiomartServer property) draw_circle_bar_plot() (in module mosaicmpi.plots) draw_circle_bar_scale() (in module mosaicmpi.plots) F factorize() (mosaicmpi.cnmf.cNMF method) fast_ols_all_cols() (in module mosaicmpi.cnmf) fetch_attributes() (mosaicmpi.biomart.BiomartDataset method) fetch_databases() (mosaicmpi.biomart.BiomartServer method) fetch_datasets() (mosaicmpi.biomart.BiomartDatabase method) (mosaicmpi.biomart.BiomartServer method) fetch_filters() (mosaicmpi.biomart.BiomartDataset method) filter_programs_rank_reduction() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) filters (mosaicmpi.biomart.BiomartDataset property) from_anndata() (mosaicmpi.Dataset class method) (mosaicmpi.dataset.Dataset class method) from_config() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) from_dataset() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) from_df() (mosaicmpi.Dataset class method) (mosaicmpi.dataset.Dataset class method) from_h5ad() (mosaicmpi.Dataset class method) (mosaicmpi.dataset.Dataset class method) from_h5ad_files() (mosaicmpi.config.Config class method) from_integration() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) from_named_datasets() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) from_network() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) from_pkl() (mosaicmpi.Network class method) (mosaicmpi.network.Network class method) from_toml() (mosaicmpi.Colors class method) (mosaicmpi.colors.Colors class method) (mosaicmpi.config.Config class method) G get_adjusted_dpi() (in module mosaicmpi.utils) get_and_check_consensus() (mosaicmpi.cnmf.cNMF method) get_approximation() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) get_category_overrepresentation() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_community_category_overrepresentation() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_community_metadata_correlation() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_community_usage() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_corr_matrix_lowertriangle() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_features_overlap_table() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_highvar_genes() (in module mosaicmpi.cnmf) get_highvar_genes_sparse() (in module mosaicmpi.cnmf) get_history() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) get_hvf_overlap_table() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_lowest_rank_programs() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_max_corr_communities() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_metadata_colors() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) get_metadata_correlation() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_metadata_df() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_nmf_iter_params() (mosaicmpi.cnmf.cNMF method) get_node_table() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_printable_metadata_type_summary() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) get_programs() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_representative_program_ids() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_representative_programs() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_request() (mosaicmpi.biomart.BiomartServer method) get_sample_entropy() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_selected_rank_program_ids() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_usages() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) get_vectorized_community_sort_key() (mosaicmpi.Network method) (mosaicmpi.network.Network method) get_verbose() (mosaicmpi.biomart.BiomartServer method) H has_cnmf_results (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) hvf (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) hvf_stats (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) I impute_knn() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) impute_zeros() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) initialize_cnmf() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) Integration (class in mosaicmpi) (class in mosaicmpi.integration) is_imputed (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) is_normalized (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) L load_df_from_npz() (in module mosaicmpi.utils) M map_gene_ids() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) module mosaicmpi mosaicmpi.biomart mosaicmpi.cli mosaicmpi.cnmf mosaicmpi.colors mosaicmpi.config mosaicmpi.dataset mosaicmpi.genesets mosaicmpi.integration mosaicmpi.nancorrmp mosaicmpi.network mosaicmpi.orphan mosaicmpi.plots mosaicmpi.utils mosaicmpi module mosaicmpi.biomart module mosaicmpi.cli module mosaicmpi.cnmf module mosaicmpi.colors module mosaicmpi.config module mosaicmpi.dataset module mosaicmpi.genesets module mosaicmpi.integration module mosaicmpi.nancorrmp module mosaicmpi.network module mosaicmpi.orphan module mosaicmpi.plots module mosaicmpi.utils module mosaicmpi_version (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) most_correlated_edge_between_datasets() (mosaicmpi.Network method) (mosaicmpi.network.Network method) N n_communities (mosaicmpi.Network property) (mosaicmpi.network.Network property) n_datasets (mosaicmpi.Integration property) (mosaicmpi.integration.Integration property) NaNCorrMp (class in mosaicmpi.nancorrmp) Network (class in mosaicmpi) (class in mosaicmpi.network) newline_wrap() (in module mosaicmpi.utils) node_to_community (mosaicmpi.Network property) (mosaicmpi.network.Network property) node_to_program() (in module mosaicmpi.utils) O order_genesets() (in module mosaicmpi.genesets) ordered_community_names (mosaicmpi.Colors property) (mosaicmpi.colors.Colors property) (mosaicmpi.Network property) (mosaicmpi.network.Network property) P patient_id_col (mosaicmpi.Dataset property) (mosaicmpi.dataset.Dataset property) plot_community_colors_legend() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) plot_community_contribution() (in module mosaicmpi.plots) plot_community_network_summary() (in module mosaicmpi.plots) plot_community_usage_heatmap() (in module mosaicmpi.plots) plot_community_usage_per_sample() (in module mosaicmpi.plots) plot_compare_integrations() (in module mosaicmpi.plots) plot_dataset_colors_legend() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) plot_feature_mean_variance() (in module mosaicmpi.plots) plot_feature_missingness() (in module mosaicmpi.plots) plot_feature_statistic_histogram() (in module mosaicmpi.plots) plot_features_upset() (in module mosaicmpi.plots) plot_geneset_heatmap() (in module mosaicmpi.plots) plot_integration_hvf_upset() (in module mosaicmpi.plots) plot_metadata_colors_legend() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) plot_metadata_correlation_community_bar() (in module mosaicmpi.plots) plot_metadata_correlation_community_network() (in module mosaicmpi.plots) plot_metadata_correlation_program_bar() (in module mosaicmpi.plots) plot_metadata_correlation_program_network() (in module mosaicmpi.plots) plot_metadata_transfer() (in module mosaicmpi.plots) plot_overrepresentation_community_bar() (in module mosaicmpi.plots) plot_overrepresentation_community_heatmap() (in module mosaicmpi.plots) plot_overrepresentation_community_network() (in module mosaicmpi.plots) plot_overrepresentation_program_bar() (in module mosaicmpi.plots) plot_overrepresentation_program_network() (in module mosaicmpi.plots) plot_pairwise_corr() (in module mosaicmpi.plots) plot_pairwise_corr_overlaid() (in module mosaicmpi.plots) plot_program_correlation_matrix() (in module mosaicmpi.plots) plot_program_network_communities() (in module mosaicmpi.plots) plot_program_network_datasets() (in module mosaicmpi.plots) plot_program_network_npatients() (in module mosaicmpi.plots) plot_program_network_nsamples() (in module mosaicmpi.plots) plot_rank_reduction() (in module mosaicmpi.plots) plot_representative_program_nes() (in module mosaicmpi.plots) plot_sample_entropy() (in module mosaicmpi.plots) plot_sample_numbers() (in module mosaicmpi.plots) plot_stability_error() (in module mosaicmpi.plots) plot_stratified_hvf_upset() (in module mosaicmpi.plots) plot_usage_heatmap() (in module mosaicmpi.plots) post_cli() (in module mosaicmpi.cli) postprocess() (mosaicmpi.cnmf.cNMF method) program_gprofiler() (in module mosaicmpi.genesets) program_ssgsea() (in module mosaicmpi.genesets) program_to_node() (in module mosaicmpi.utils) programs_in_graph (mosaicmpi.Network property) (mosaicmpi.network.Network property) prune_communities() (mosaicmpi.Network method) (mosaicmpi.network.Network method) R read_communities_from_toml() (mosaicmpi.Network method) (mosaicmpi.network.Network method) recursive_update() (in module mosaicmpi.config) refit_spectra() (mosaicmpi.cnmf.cNMF method) refit_usage() (mosaicmpi.cnmf.cNMF method) remove_cnmf_results() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) remove_unfactorizable_features() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) remove_unfactorizable_observations() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) reset_community_colors() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) S sample_to_patient (mosaicmpi.Integration property) (mosaicmpi.integration.Integration property) save_df_to_npz() (in module mosaicmpi.utils) save_df_to_text() (in module mosaicmpi.utils) save_fig() (in module mosaicmpi.utils) save_nmf_iter_params() (mosaicmpi.cnmf.cNMF method) search() (mosaicmpi.biomart.BiomartDataset method) select_hvf() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) select_hvf_cnmf() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) select_hvf_stdeconvolve() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) select_k_values() (mosaicmpi.Integration method) (mosaicmpi.integration.Integration method) selected_k (mosaicmpi.Integration property) (mosaicmpi.integration.Integration property) set_verbose() (mosaicmpi.biomart.BiomartServer method) show_attributes() (mosaicmpi.biomart.BiomartDataset method) show_attributes_by_page() (mosaicmpi.biomart.BiomartDataset method) show_databases() (mosaicmpi.biomart.BiomartServer method) show_datasets() (mosaicmpi.biomart.BiomartDatabase method) (mosaicmpi.biomart.BiomartServer method) show_filters() (mosaicmpi.biomart.BiomartDataset method) start_logging() (in module mosaicmpi.utils) T to_df() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) to_pkl() (mosaicmpi.Network method) (mosaicmpi.network.Network method) to_toml() (mosaicmpi.Colors method) (mosaicmpi.colors.Colors method) (mosaicmpi.config.Config method) transfer_labels() (mosaicmpi.Network method) (mosaicmpi.network.Network method) U update_obs() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) V validate_cnmf_prediction_errors() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) validate_feature_stats() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) verbose (mosaicmpi.biomart.BiomartServer property) W write_communities_toml() (mosaicmpi.Network method) (mosaicmpi.network.Network method) write_community_network_graphml() (mosaicmpi.Network method) (mosaicmpi.network.Network method) write_h5ad() (mosaicmpi.Dataset method) (mosaicmpi.dataset.Dataset method) write_program_network_graphml() (mosaicmpi.Network method) (mosaicmpi.network.Network method)
