Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | P | R | S | T | U | W _ __init__() (anndict.adata_dict.adata_dict.AdataDict method) A adata_dict_fapply() (in module anndict.adata_dict) AdataDict (class in anndict) (class in anndict.adata_dict.adata_dict) add_blank_image_to_adata() (in module anndict.utils) add_col_to_adata_obs() (in module anndict.utils) add_col_to_adata_var() (in module anndict.utils) add_col_to_pd_df() (in module anndict.utils) add_stratification() (anndict.AdataDict method) (in module anndict.adata_dict) ai_annotate() (in module anndict.annotate.cells.de_novo) ai_annotate_biological_process() (in module anndict.annotate) ai_annotate_biological_process_adata_dict() (in module anndict.wrappers) ai_annotate_by_comparison() (in module anndict.annotate.cells.de_novo) ai_annotate_cell_sub_type() (in module anndict.annotate) ai_annotate_cell_sub_type_adata_dict() (in module anndict.wrappers) ai_annotate_cell_type() (in module anndict.annotate) ai_annotate_cell_type_adata_dict() (in module anndict.wrappers) ai_annotate_cell_type_by_comparison() (in module anndict.annotate) ai_annotate_from_expected_cell_types() (in module anndict.annotate) ai_biological_process() (in module anndict.annotate) ai_cell_type() (in module anndict.annotate) ai_cell_types_by_comparison() (in module anndict.annotate) ai_compare_cell_type_labels_pairwise() (in module anndict.annotate) ai_compare_cell_type_labels_pairwise_adata_dict() (in module anndict.wrappers) ai_determine_leiden_resolution() (in module anndict.annotate) ai_determine_leiden_resolution_adata_dict() (in module anndict.wrappers) ai_from_expected_cell_types() (in module anndict.annotate) ai_make_cell_type_gene_list() (in module anndict.annotate) ai_unify_labels() (in module anndict) anndict.annotate module anndict.annotate.genes module annotate_gene_groups_with_ai_biological_process() (in module anndict.plot) B build_adata_dict() (in module anndict.adata_dict) build_adata_from_transcript_positions() (in module anndict.utils) build_adata_from_visium() (in module anndict.utils) C calculate_umap_adata_dict() (in module anndict.wrappers) call_llm() (in module anndict) cell_type_marker_gene_score() (in module anndict.annotate) check_structure() (anndict.AdataDict method) concatenate_adata_dict() (in module anndict.adata_dict) configure_llm_backend() (in module anndict) convert_obs_col_to_category() (in module anndict.utils) convert_obs_col_to_string() (in module anndict.utils) convert_obs_index_to_str() (in module anndict.utils) copy() (anndict.AdataDict method) create_anndata() (in module anndict.utils) create_color_map() (in module anndict.utils) create_label_df() (in module anndict.annotate) create_label_hierarchy() (in module anndict) create_label_hierarchy_adata_dict() (in module anndict.wrappers) D display_html_summary() (in module anndict.utils) display_html_summary_adata_dict() (in module anndict.wrappers) E enforce_semantic_list() (in module anndict.utils) ensure_label_consistency_adata() (in module anndict) ensure_label_consistency_adata_dict() (in module anndict.wrappers) ensure_label_consistency_main() (in module anndict) F fapply() (anndict.AdataDict method) fapply_return() (anndict.AdataDict method) filter_gene_list() (in module anndict.utils) flatten() (anndict.AdataDict method) G get_adata_columns() (in module anndict.utils) get_llm_config() (in module anndict) get_slurm_cores() (in module anndict.utils) get_steps_and_coords() (in module anndict.utils) H harmony_label_transfer() (in module anndict.annotate) harmony_label_transfer_adata_dict() (in module anndict.wrappers) hierarchy (anndict.AdataDict property) I index_bool() (anndict.AdataDict method) K kappa_adata() (in module anndict.annotate) krippendorff_alpha_adata() (in module anndict.annotate) L leiden_adata_dict() (in module anndict.wrappers) leiden_sub_cluster() (in module anndict.wrappers) leiden_sub_cluster_adata_dict() (in module anndict.wrappers) log_transform_adata_dict() (in module anndict.wrappers) M make_names() (in module anndict.utils) map_cell_type_labels_to_simplified_set() (in module anndict) map_gene_labels_to_simplified_set() (in module anndict) module anndict.annotate anndict.annotate.genes module_score_barplot() (in module anndict.plot) module_score_umap() (in module anndict.plot) N neighbors_adata_dict() (in module anndict.wrappers) normalize_adata_dict() (in module anndict.wrappers) normalize_label() (in module anndict.utils) normalize_string() (in module anndict.utils) P pca_adata_dict() (in module anndict.wrappers) pca_density_adata_dict() (in module anndict.wrappers) pca_density_filter_adata() (in module anndict.utils) pca_density_filter_main() (in module anndict.utils) plot_confusion_matrix() (in module anndict.plot) plot_confusion_matrix_adata_dict() (in module anndict.wrappers) plot_confusion_matrix_from_adata() (in module anndict.plot) plot_grouped_average() (in module anndict.plot) plot_grouped_average_adata_dict() (in module anndict.wrappers) plot_label_changes() (in module anndict.plot) plot_label_changes_adata_dict() (in module anndict.wrappers) plot_model_agreement() (in module anndict.plot) plot_model_agreement_categorical() (in module anndict.plot) plot_sankey() (in module anndict.plot), [1], [2] plot_sankey_adata_dict() (in module anndict.wrappers) plot_training_history() (in module anndict.plot) plot_umap_adata_dict() (in module anndict.wrappers) populate_sparse_array() (in module anndict.utils) process_gene_counts() (in module anndict.utils) R rank_genes_groups_adata_dict() (in module anndict.wrappers) read_adata_dict() (in module anndict.adata_dict) read_adata_dict_from_h5ad() (in module anndict.adata_dict) read_transcript_coords() (in module anndict.utils) remove_genes() (in module anndict.utils) remove_genes_adata_dict() (in module anndict.wrappers) retry_call_llm() (in module anndict) S sample_adata_dict() (in module anndict.utils) sample_and_drop() (in module anndict.utils) sample_and_drop_adata_dict() (in module anndict.wrappers) save_sankey() (in module anndict.plot), [1], [2] save_sankey_adata_dict() (in module anndict.wrappers) scale_adata_dict() (in module anndict.wrappers) set_hierarchy() (anndict.AdataDict method) set_high_variance_genes_adata_dict() (in module anndict.wrappers) set_obs_index() (anndict.AdataDict method) set_var_index() (anndict.AdataDict method) simplify_obs_column() (in module anndict) simplify_obs_column_adata_dict() (in module anndict.wrappers) simplify_var_index() (in module anndict) simplify_var_index_adata_dict() (in module anndict.wrappers) stable_label() (in module anndict.utils) stable_label_adata() (in module anndict.utils) summarize_metadata() (in module anndict.utils) summarize_metadata_adata_dict() (in module anndict.wrappers) T train_label_classifier() (in module anndict.annotate) transfer_labels_using_classifier() (in module anndict.annotate) U uce_adata() (in module anndict.utils) W write_adata_dict() (in module anndict.adata_dict)
