Index A | C | D | E | F | G | H | I | K | L | M | P | S | T | U | V | W A add_pmhc_pseudosequence_to_dataframe() (in module tcr_deep_insight.tl) add_tcr_pseudosequence_to_dataframe() (in module tcr_deep_insight.tl) C calculate_cluster_additional_information() (tcr_deep_insight.tl.TDIResult method) CDR123 (tcr_deep_insight.model.TCR_BERT_ENCODING attribute) cdr3a (tcr_deep_insight.TCR property) cdr3b (tcr_deep_insight.TCR property) CLS (tcr_deep_insight.model.TCR_BERT_POOLING attribute) cluster_label (tcr_deep_insight.tl.TDIResult property) cluster_tcr() (in module tcr_deep_insight.tl) cluster_tcr_from_reference() (in module tcr_deep_insight.tl) convert_ids_to_tokens() (tcr_deep_insight.model.TRabTokenizerForVJCDR3 method) convert_tokens_to_ids() (tcr_deep_insight.model.TRabTokenizerForVJCDR3 method) create_fig() (in module tcr_deep_insight.pl) create_subplots() (in module tcr_deep_insight.pl) D D (tcr_deep_insight.tl.TDIResult property) data (tcr_deep_insight.tl.TDIResult property) deserialize() (tcr_deep_insight.TCR class method) E evaluate() (tcr_deep_insight.model.TRabModelingBertForVJCDR3Trainer method) F FAISS_INDEX_BACKEND (class in tcr_deep_insight.tl) fit() (tcr_deep_insight.model.TRabModelingBertForVJCDR3Trainer method) FLAT (tcr_deep_insight.tl.FAISS_INDEX_BACKEND attribute) forward() (tcr_deep_insight.model.TRabModelingBertForPseudoSequence method) (tcr_deep_insight.model.TRabModelingBertForVJCDR3 method) from_string() (tcr_deep_insight.TCR class method) G get_human_config() (in module tcr_deep_insight.model.modeling_bert) get_pretrained_tcr_embedding() (in module tcr_deep_insight.tl) get_tcrs_by_cluster_index() (tcr_deep_insight.tl.TDIResult method) get_tcrs_for_cluster() (tcr_deep_insight.tl.TDIResult method) gex_adata (tcr_deep_insight.tl.TDIResult property) GEXModelingVAE (in module tcr_deep_insight.model) H HUMAN (tcr_deep_insight.SPECIES attribute) human_gex_reference_v2() (in module tcr_deep_insight.data) human_tcr_reference_v2() (in module tcr_deep_insight.data) I I (tcr_deep_insight.tl.TDIResult property) individual (tcr_deep_insight.TCR property) inject_labels_for_tcr_cluster_adata() (in module tcr_deep_insight.tl) K KMEANS (tcr_deep_insight.tl.FAISS_INDEX_BACKEND attribute) L load_from_disk() (tcr_deep_insight.tl.TDIResult class method) M MAX (tcr_deep_insight.model.TCR_BERT_POOLING attribute) MEAN (tcr_deep_insight.model.TCR_BERT_POOLING attribute) MOUSE (tcr_deep_insight.SPECIES attribute) mouse_gex_reference_v1() (in module tcr_deep_insight.data) mouse_tcr_reference_v1() (in module tcr_deep_insight.data) P plot_cdr3_sequence() (in module tcr_deep_insight.pl) plot_selected_tcrs() (in module tcr_deep_insight.pl) POOL (tcr_deep_insight.model.TCR_BERT_POOLING attribute) S save_to_disk() (tcr_deep_insight.tl.TDIResult method) select() (tcr_deep_insight.tl.TDIResult method) serialize() (tcr_deep_insight.TCR method) set_plotting_params() (in module tcr_deep_insight.pl) SPECIES (class in tcr_deep_insight) species (tcr_deep_insight.TCR property) SUM (tcr_deep_insight.model.TCR_BERT_POOLING attribute) T TCR (class in tcr_deep_insight) tcr_adata (tcr_deep_insight.tl.TDIResult property) tcr_adata_to_datasets() (in module tcr_deep_insight.tl) TCR_BERT_ENCODING (class in tcr_deep_insight.model) TCR_BERT_POOLING (class in tcr_deep_insight.model) tcr_dataframe_to_datasets() (in module tcr_deep_insight.tl) tcr_df (tcr_deep_insight.tl.TDIResult property) TDIResult (class in tcr_deep_insight.tl) to_dataset() (tcr_deep_insight.model.TRabTokenizerForVJCDR3 method) to_embedding_tcr_only() (in module tcr_deep_insight.tl) to_embedding_tcr_only_from_pandas() (in module tcr_deep_insight.tl) to_pandas_dataframe_cluster_index() (tcr_deep_insight.tl.TDIResult method) to_pandas_dataframe_tcr() (tcr_deep_insight.tl.TDIResult method) to_string() (tcr_deep_insight.TCR method) to_tcr_string() (tcr_deep_insight.TCR method) TRA (tcr_deep_insight.model.TCR_BERT_POOLING attribute) TRabCollatorForVJCDR3 (class in tcr_deep_insight.model) TRabModelingBertForPseudoSequence (class in tcr_deep_insight.model) TRabModelingBertForVJCDR3 (class in tcr_deep_insight.model) TRabModelingBertForVJCDR3Trainer (class in tcr_deep_insight.model) TRabTokenizerForVJCDR3 (class in tcr_deep_insight.model) traj (tcr_deep_insight.TCR property) trav (tcr_deep_insight.TCR property) TRB (tcr_deep_insight.model.TCR_BERT_POOLING attribute) trbj (tcr_deep_insight.TCR property) trbv (tcr_deep_insight.TCR property) U unique_tcr_by_individual() (in module tcr_deep_insight.pp) update_anndata() (in module tcr_deep_insight.pp) V VJCDR3 (tcr_deep_insight.model.TCR_BERT_ENCODING attribute) W WEIGHTED (tcr_deep_insight.model.TCR_BERT_POOLING attribute)