Index A | B | C | D | E | F | G | H | I | L | M | O | P | Q | R | S | T | V | W | Z A aggregate_counts() (in module scimilarity.visualizations) align_dataset() (in module scimilarity.utils) all_pair_similarities() (in module scimilarity.ontologies) annotate_cell_index() (scimilarity.cell_query.CellQuery method) annotate_dataset() (scimilarity.cell_annotation.CellAnnotation method) append_annotation() (scimilarity.zarr_dataset.ZarrDataset method) append_matrix() (scimilarity.zarr_dataset.ZarrDataset method) append_X() (scimilarity.zarr_dataset.ZarrDataset method) assign_colors() (in module scimilarity.visualizations) assign_size() (in module scimilarity.visualizations) assign_suffix() (in module scimilarity.visualizations) B blocklist_celltypes() (scimilarity.cell_annotation.CellAnnotation method) build_knn() (scimilarity.cell_annotation.CellAnnotation method) C categorize_and_sort_by_score() (in module scimilarity.utils) CellAnnotation (class in scimilarity.cell_annotation) CellEmbedding (class in scimilarity.cell_embedding) CellQuery (class in scimilarity.cell_query) CellSearchKNN (class in scimilarity.cell_search_knn) circ_dict2data() (in module scimilarity.visualizations) clean_diseases() (in module scimilarity.utils) clean_tissues() (in module scimilarity.utils) col_slice_csc() (scimilarity.zarr_dataset.ZarrDataset method) collate() (scimilarity.anndata_data_models.MetricLearningDataModule method) (scimilarity.zarr_data_models.MetricLearningDataModule method) compile_sample_metadata() (scimilarity.cell_query.CellQuery method) configure_optimizers() (scimilarity.training_models.MetricLearning method) consolidate_duplicate_symbols() (in module scimilarity.utils) create_embeddings_tiledb() (scimilarity.cell_query.CellQuery method) D dataset_info (scimilarity.zarr_dataset.ZarrDataset property) Decoder (class in scimilarity.nn_models) draw_circles() (in module scimilarity.visualizations) E Encoder (class in scimilarity.nn_models) F filter_cells() (in module scimilarity.utils) find_most_viable_parent() (in module scimilarity.ontologies) forward() (scimilarity.interpreter.SimpleDist method) (scimilarity.nn_models.Decoder method) (scimilarity.nn_models.Encoder method) (scimilarity.training_models.MetricLearning method) (scimilarity.training_models.TripletLoss method) G get_all_ancestors() (in module scimilarity.ontologies) get_all_descendants() (in module scimilarity.ontologies) get_annotation_column() (scimilarity.zarr_dataset.ZarrDataset method) get_annotation_index() (scimilarity.zarr_dataset.ZarrDataset method) get_asw() (scimilarity.triplet_selector.TripletSelector method) get_attributions() (scimilarity.interpreter.Interpreter method) get_cell() (scimilarity.zarr_dataset.ZarrDataset method) get_centroid() (in module scimilarity.utils) get_children() (in module scimilarity.ontologies) get_children_data() (in module scimilarity.visualizations) get_cluster_centroids() (in module scimilarity.utils) get_col() (scimilarity.zarr_dataset.ZarrDataset method) get_counts() (scimilarity.zarr_dataset.ZarrDataset method) get_dist2centroid() (in module scimilarity.utils) get_embeddings() (scimilarity.cell_embedding.CellEmbedding method) get_gene() (scimilarity.zarr_dataset.ZarrDataset method) get_id_mapper() (in module scimilarity.ontologies) get_layer_cell() (scimilarity.zarr_dataset.ZarrDataset method) get_layer_gene() (scimilarity.zarr_dataset.ZarrDataset method) get_losses() (scimilarity.training_models.MetricLearning method) get_lowest_common_ancestor() (in module scimilarity.ontologies) get_matrix() (scimilarity.zarr_dataset.ZarrDataset method) get_mixed_loss() (scimilarity.training_models.MetricLearning method) get_nearest_neighbors() (scimilarity.cell_search_knn.CellSearchKNN method) get_obs() (scimilarity.zarr_dataset.ZarrDataset method) get_parents() (in module scimilarity.ontologies) get_precomputed_embeddings() (scimilarity.cell_query.CellQuery method) get_predictions_knn() (scimilarity.cell_annotation.CellAnnotation method) get_ranked_genes() (scimilarity.interpreter.Interpreter method) get_row() (scimilarity.zarr_dataset.ZarrDataset method) get_sampler_weights() (scimilarity.anndata_data_models.MetricLearningDataModule method) (scimilarity.zarr_data_models.MetricLearningDataModule method) get_siblings() (in module scimilarity.ontologies) get_triplets() (scimilarity.triplet_selector.TripletSelector method) get_triplets_idx() (scimilarity.triplet_selector.TripletSelector method) get_uns() (scimilarity.zarr_dataset.ZarrDataset method) get_var() (scimilarity.zarr_dataset.ZarrDataset method) get_X() (scimilarity.zarr_dataset.ZarrDataset method) H hardest_negative() (scimilarity.triplet_selector.TripletSelector method) hits_circles() (in module scimilarity.visualizations) hits_heatmap() (in module scimilarity.visualizations) I import_cell_ontology() (in module scimilarity.ontologies) import_doid_ontology() (in module scimilarity.ontologies) import_mondo_ontology() (in module scimilarity.ontologies) import_uberon_ontology() (in module scimilarity.ontologies) Interpreter (class in scimilarity.interpreter) L load_knn_index() (scimilarity.cell_search_knn.CellSearchKNN method) load_state() (scimilarity.nn_models.Decoder method) (scimilarity.nn_models.Encoder method) (scimilarity.training_models.MetricLearning method) lognorm_counts() (in module scimilarity.utils) M MetricLearning (class in scimilarity.training_models) MetricLearningDataModule (class in scimilarity.anndata_data_models) (class in scimilarity.zarr_data_models) module scimilarity.anndata_data_models scimilarity.cell_annotation scimilarity.cell_embedding scimilarity.cell_query scimilarity.cell_search_knn scimilarity.interpreter scimilarity.nn_models scimilarity.ontologies scimilarity.training_models scimilarity.triplet_selector scimilarity.utils scimilarity.visualizations scimilarity.zarr_data_models scimilarity.zarr_dataset O obs (scimilarity.zarr_dataset.ZarrDataset property) obs_index (scimilarity.zarr_dataset.ZarrDataset property) on_test_epoch_end() (scimilarity.training_models.MetricLearning method) on_test_epoch_start() (scimilarity.training_models.MetricLearning method) on_validation_epoch_end() (scimilarity.training_models.MetricLearning method) on_validation_epoch_start() (scimilarity.training_models.MetricLearning method) ontology_silhouette_width() (in module scimilarity.ontologies) ontology_similarity() (in module scimilarity.ontologies) optimize_tiledb_array() (in module scimilarity.utils) P pdist() (scimilarity.triplet_selector.TripletSelector method) plot_ranked_genes() (scimilarity.interpreter.Interpreter method) pseudobulk_anndata() (in module scimilarity.utils) Q query_tiledb_df() (in module scimilarity.utils) R random_negative() (scimilarity.triplet_selector.TripletSelector method) reset_knn() (scimilarity.cell_annotation.CellAnnotation method) row_slice_csr() (scimilarity.zarr_dataset.ZarrDataset method) S safelist_celltypes() (scimilarity.cell_annotation.CellAnnotation method) save_state() (scimilarity.nn_models.Decoder method) (scimilarity.nn_models.Encoder method) scDataset (class in scimilarity.anndata_data_models) (class in scimilarity.zarr_data_models) scimilarity.anndata_data_models module scimilarity.cell_annotation module scimilarity.cell_embedding module scimilarity.cell_query module scimilarity.cell_search_knn module scimilarity.interpreter module scimilarity.nn_models module scimilarity.ontologies module scimilarity.training_models module scimilarity.triplet_selector module scimilarity.utils module scimilarity.visualizations module scimilarity.zarr_data_models module scimilarity.zarr_dataset module search_centroid_exhaustive() (scimilarity.cell_query.CellQuery method) search_centroid_nearest() (scimilarity.cell_query.CellQuery method) search_cluster_centroids_exhaustive() (scimilarity.cell_query.CellQuery method) search_cluster_centroids_nearest() (scimilarity.cell_query.CellQuery method) search_exhaustive() (scimilarity.cell_query.CellQuery method) search_nearest() (scimilarity.cell_query.CellQuery method) semihard_negative() (scimilarity.triplet_selector.TripletSelector method) set_annotation() (scimilarity.zarr_dataset.ZarrDataset method) set_matrix() (scimilarity.zarr_dataset.ZarrDataset method) set_X() (scimilarity.zarr_dataset.ZarrDataset method) shape (scimilarity.zarr_dataset.ZarrDataset property) SimpleDist (class in scimilarity.interpreter) slice_across() (scimilarity.zarr_dataset.ZarrDataset method) slice_coo() (scimilarity.zarr_dataset.ZarrDataset method) slice_with() (scimilarity.zarr_dataset.ZarrDataset method) subset_by_frequency() (in module scimilarity.utils) subset_by_unique_values() (in module scimilarity.utils) subset_nodes_to_set() (in module scimilarity.ontologies) subset_valid_terms() (scimilarity.anndata_data_models.MetricLearningDataModule method) T test_dataloader() (scimilarity.anndata_data_models.MetricLearningDataModule method) (scimilarity.zarr_data_models.MetricLearningDataModule method) test_step() (scimilarity.training_models.MetricLearning method) train_dataloader() (scimilarity.anndata_data_models.MetricLearningDataModule method) (scimilarity.zarr_data_models.MetricLearningDataModule method) training_step() (scimilarity.training_models.MetricLearning method) TripletLoss (class in scimilarity.training_models) TripletSelector (class in scimilarity.triplet_selector) V val_dataloader() (scimilarity.anndata_data_models.MetricLearningDataModule method) (scimilarity.zarr_data_models.MetricLearningDataModule method) validation_step() (scimilarity.training_models.MetricLearning method) var (scimilarity.zarr_dataset.ZarrDataset property) var_index (scimilarity.zarr_dataset.ZarrDataset property) W write_array_to_tiledb() (in module scimilarity.utils) write_csr_to_tiledb() (in module scimilarity.utils) Z ZarrDataset (class in scimilarity.zarr_dataset)