Index A | C | D | E | F | G | L | M | N | P | R | S | T | U | W A add_annotations() (in module scarches.utils) add_new_cell_type() (scarches.models.scPoli method) C classify() (scarches.models.scPoli method) create_deposition() (in module scarches.zenodo.deposition) D delete_deposition() (in module scarches.zenodo.deposition) differential_expression() (scarches.models.TOTALVI method) download_file() (in module scarches.zenodo.file) download_model() (in module scarches.zenodo) E EXPIMAP (class in scarches.models) F from_scvi_model() (scarches.models.SCANVI class method) G get_all_deposition_ids() (in module scarches.zenodo.deposition) get_asw() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_classification_accuracy() (scarches.plotting.SCVI_EVAL method) get_conditional_embeddings() (scarches.models.scPoli method) get_ebm() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_f1_score() (scarches.plotting.SCVI_EVAL method) get_feature_correlation_matrix() (scarches.models.TOTALVI method) get_knn_purity() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_latent() (scarches.models.EXPIMAP method) (scarches.models.scPoli method) get_latent_library_size() (scarches.models.TOTALVI method) get_latent_score() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_likelihood_parameters() (scarches.models.TOTALVI method) get_model_arch() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_nmi() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) get_normalized_expression() (scarches.models.TOTALVI method) get_protein_background_mean() (scarches.models.TOTALVI method) get_protein_foreground_probability() (scarches.models.TOTALVI method) get_prototypes_info() (scarches.models.scPoli method) get_recon_loss() (scarches.models.scPoli method) L label_encoder() (in module scarches.dataset) latent_as_anndata() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) latent_directions() (scarches.models.EXPIMAP method) latent_enrich() (scarches.models.EXPIMAP method) load_query_data() (scarches.models.EXPIMAP class method) (scarches.models.scPoli class method) M mask_genes() (scarches.models.EXPIMAP method) minify_adata() (scarches.models.SCANVI method) (scarches.models.SCVI method) module scarches.dataset scarches.plotting scarches.utils scarches.zenodo scarches.zenodo.deposition scarches.zenodo.file N nonzero_terms() (scarches.models.EXPIMAP method) P plot_abs_bfs() (in module scarches.plotting) plot_history() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) plot_latent() (scarches.plotting.SCVI_EVAL method) (scarches.plotting.TRVAE_EVAL method) posterior_predictive_sample() (scarches.models.TOTALVI method) predict() (scarches.models.SCANVI method) publish_deposition() (in module scarches.zenodo.deposition) R remove_sparsity() (in module scarches.dataset) S sankey_diagram() (in module scarches.plotting) SCANVI (class in scarches.models) scarches.dataset module scarches.plotting module scarches.utils module scarches.zenodo module scarches.zenodo.deposition module scarches.zenodo.file module scPoli (class in scarches.models) SCVI (class in scarches.models) SCVI_EVAL (class in scarches.plotting) setup_anndata() (scarches.models.SCANVI class method) (scarches.models.SCVI class method) (scarches.models.TOTALVI class method) setup_mudata() (scarches.models.TOTALVI class method) shot_surgery() (scarches.models.scPoli class method) T term_genes() (scarches.models.EXPIMAP method) TOTALVI (class in scarches.models) train() (scarches.models.EXPIMAP method) (scarches.models.SCANVI method) (scarches.models.scPoli method) (scarches.models.TOTALVI method) (scarches.models.TRVAE method) TRVAE (class in scarches.models) TRVAE_EVAL (class in scarches.plotting) trVAEDataset (in module scarches.dataset) U update_deposition() (in module scarches.zenodo.deposition) update_terms() (scarches.models.EXPIMAP method) upload_file() (in module scarches.zenodo.file) upload_model() (in module scarches.zenodo) W weighted_knn_trainer() (in module scarches.utils) weighted_knn_transfer() (in module scarches.utils)