Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U A aggregate_by_taxonomic_level() (in module momics.taxonomy) alpha_diversity_parametrized() (in module momics.diversity) alpha_input() (in module momics.diversity) alpha_plot() (in module momics.plotting) av_alpha_plot() (in module momics.plotting) B beta_diversity_parametrized() (in module momics.diversity) beta_plot() (in module momics.plotting) beta_plot_pc() (in module momics.plotting) beta_plot_pc_granular() (in module momics.plotting) build_interaction_graphs() (in module momics.networks) bytes_to_df() (in module momics.loader.utils) C calculate_alpha_diversity() (in module momics.diversity) calculate_shannon_index() (in module momics.diversity) change_legend_labels() (in module momics.plotting) check_index_names() (in module momics.utils) clean_histories_for_display() (momics.galaxy.RemGalaxy method) clean_metadata() (in module momics.metadata) clean_tax_row() (in module momics.taxonomy) close_server() (in module momics.panel_utils) compute_bray_curtis() (in module momics.taxonomy) create_indicators_diversity() (in module momics.panel_utils) create_indicators_landing_page() (in module momics.panel_utils) cut_xaxis_labels() (in module momics.plotting) D diversity_input() (in module momics.diversity) diversity_select_widgets() (in module momics.panel_utils) E enhance_metadata() (in module momics.metadata) extract_all_datafiles() (in module momics.loader.ro_crates) extract_data_by_name() (in module momics.loader.ro_crates) extract_season() (in module momics.metadata) extract_season_single() (in module momics.metadata) F fdr_pvals() (in module momics.taxonomy) fill_na_for_object_columns() (in module momics.metadata) fill_taxonomy_placeholders() (in module momics.taxonomy) filter_data() (in module momics.metadata) filter_metadata_table() (in module momics.metadata) filter_metadata_terms() (in module momics.metadata) find_taxa_in_table() (in module momics.diversity) fold_legend_labels_from_series() (in module momics.plotting) G Gecco (class in momics.galaxy) get_datasets() (momics.galaxy.RemGalaxy method) get_datasets_by_key() (momics.galaxy.RemGalaxy method) get_histories() (momics.galaxy.RemGalaxy method) get_key_column() (in module momics.diversity) get_metadata() (in module momics.metadata) get_metadata_udal() (in module momics.metadata) get_notebook_environment() (in module momics.utils) get_rocrate_data() (in module momics.loader.ro_crates) get_rocrate_metadata_gh() (in module momics.loader.ro_crates) get_sankey() (in module momics.plotting) H handle_create_history() (momics.galaxy.Gecco method) handle_get_datasets() (momics.galaxy.Gecco method) handle_get_histories() (momics.galaxy.Gecco method) handle_login() (momics.galaxy.Gecco method) handle_submit_gecco() (momics.galaxy.Gecco method) handle_update_current_file_name() (momics.galaxy.Gecco method) handle_update_current_history_id() (momics.galaxy.Gecco method) handle_update_current_history_name() (momics.galaxy.Gecco method) handle_upload_dataset() (momics.galaxy.Gecco method) hvplot_alpha_diversity() (in module momics.plotting) hvplot_average_per_factor() (in module momics.plotting) hvplot_bgcs_violin() (in module momics.plotting) hvplot_heatmap() (in module momics.plotting) hvplot_plot_pcoa_black() (in module momics.plotting) I init_setup() (in module momics.utils) install_colab_packages() (in module momics.utils) interaction_to_graph() (in module momics.networks) interaction_to_graph_with_pvals() (in module momics.networks) is_ipython() (in module momics.utils) is_port_in_use() (in module momics.panel_utils) L load_and_clean() (in module momics.utils) load_parquets() (in module momics.loader.parquets) load_parquets_udal() (in module momics.loader.parquets) logger (in module momics.taxonomy) M map_taxa_up() (in module momics.taxonomy) memory_load() (in module momics.utils) memory_usage() (in module momics.utils) merge_source_mat_id_to_data() (in module momics.metadata) module momics momics.constants momics.diversity momics.galaxy momics.loader.parquets momics.loader.ro_crates momics.loader.utils momics.metadata momics.networks momics.panel_utils momics.plotting momics.stats momics.taxonomy momics.utils momics module momics.constants module momics.diversity module momics.galaxy module momics.loader.parquets module momics.loader.ro_crates module momics.loader.utils module momics.metadata module momics.networks module momics.panel_utils module momics.plotting module momics.stats module momics.taxonomy module momics.utils module mpl_alpha_diversity() (in module momics.plotting) mpl_average_per_factor() (in module momics.plotting) mpl_bgcs_violin() (in module momics.plotting) mpl_plot_heatmap() (in module momics.plotting) N normalize_abundance() (in module momics.taxonomy) P pairwise_jaccard_lower_triangle() (in module momics.networks) pivot_taxonomic_data() (in module momics.taxonomy) plot_association_histogram() (in module momics.stats) plot_domain_abundance() (in module momics.plotting) plot_fdr() (in module momics.stats) plot_network() (in module momics.plotting) plot_pcoa_black() (in module momics.plotting) plot_tsne() (in module momics.plotting) prevalence_cutoff() (in module momics.taxonomy) prevalence_cutoff_taxonomy() (in module momics.taxonomy) process_collection_date() (in module momics.metadata) R rarefy_table() (in module momics.taxonomy) reconfig_logger() (in module momics.utils) RemGalaxy (class in momics.galaxy) remove_high_taxa() (in module momics.taxonomy) rename_metadata_terms_vre() (in module momics.metadata) run_permanova() (in module momics.diversity) S separate_taxonomy() (in module momics.taxonomy) separate_taxonomy_eukaryota() (in module momics.taxonomy) serve_app() (in module momics.panel_utils) set_dataset() (momics.galaxy.RemGalaxy method) set_galaxy_env() (momics.galaxy.RemGalaxy method) set_history() (momics.galaxy.RemGalaxy method) set_tool() (momics.galaxy.RemGalaxy method) setup_ipython() (in module momics.utils) shannon_index() (in module momics.diversity) show_job_status() (momics.galaxy.RemGalaxy method) spearman_from_taxonomy() (in module momics.stats) split_metadata() (in module momics.taxonomy) split_taxonomic_data() (in module momics.taxonomy) split_taxonomic_data_pivoted() (in module momics.taxonomy) split_taxonomy() (in module momics.taxonomy) T tax_finder_selector() (in module momics.panel_utils) taxon_in_table() (in module momics.taxonomy) taxonomy_common_preprocess01() (in module momics.utils) U update_subset_indicator() (in module momics.diversity) update_taxa_count_indicator() (in module momics.diversity) upload_file() (momics.galaxy.RemGalaxy method)