Welcome to TCR-DeepInsight’s documentation!

Installation

Click here to view a brief TCR-DeepInsight installation guide.

Installation

API

Click here to view a brief TCR-DeepInsight API documentation

API

Knowledge base

Click here to view a TCR-DeepInsight knowledge base.

Knowledge base

GitHub

Ask questions, report bugs, and contribute to TCR-DeepInsight at our GitHub repository.

https://github.com/WanluLiuLab/TCR-DeepInsight

Contents

• Introduction
  • Rationale
  • Dataset
  • Update Plan
    • Change log
• Installation
  • Install from PyPI
  • Install from source
• Usage
• Example datasets
• Pretrained models
• Tutorial
  • Contents
    • Training T cell receptor alpha and beta chains (TCRαβ) seqeunce by BERT
      • Load the reference dataset
      • Training the TCR sequence by BERT
      • Obtaining TCR sequence embedding
    • Training Gene Expression (GEX) data by VAE
      • Load the reference dataset
      • Construct and train the GEX model
      • Extract the GEX embedding and Save the trained model
      • Clustering and UMAP visualization
    • Clustering TCRαβ and GEX
      • Load the reference dataset
      • Searching for cGxTr clusters without any constraints
      • Searching for cGxTr clusters with at least one common HLA alleles
      • Searching for cGxTr clusters with unique disease type
      • Searching for cGxTr clusters with constrains on TCRs
      • Combining the clustering constrains
  • Processing 10x Immune Profiling Data
  • TCR Tutorial
  • GEX Tutorial
  • TrGx Clustering Tutorial
• API
  • SPECIES
    • SPECIES.HUMAN
    • SPECIES.MOUSE
  • TCR
    • TCR.cdr3a
    • TCR.cdr3b
    • TCR.deserialize()
    • TCR.from_string()
    • TCR.individual
    • TCR.serialize()
    • TCR.species
    • TCR.to_string()
    • TCR.to_tcr_string()
    • TCR.traj
    • TCR.trav
    • TCR.trbj
    • TCR.trbv
  • Preprocessing
    • update_anndata()
    • unique_tcr_by_individual()
  • Data
    • human_gex_reference_v2()
    • human_tcr_reference_v2()
    • mouse_gex_reference_v1()
    • mouse_tcr_reference_v1()
  • Tool
    • add_tcr_pseudosequence_to_dataframe()
    • add_pmhc_pseudosequence_to_dataframe()
    • tcr_adata_to_datasets()
    • tcr_dataframe_to_datasets()
    • to_embedding_tcr_only()
    • to_embedding_tcr_only_from_pandas()
    • get_pretrained_tcr_embedding()
    • Clustering
      • cluster_tcr()
      • cluster_tcr_from_reference()
      • inject_labels_for_tcr_cluster_adata()
      • TDIResult
        • TDIResult.D
        • TDIResult.I
        • TDIResult.calculate_cluster_additional_information()
        • TDIResult.cluster_label
        • TDIResult.data
        • TDIResult.get_tcrs_by_cluster_index()
        • TDIResult.get_tcrs_for_cluster()
        • TDIResult.gex_adata
        • TDIResult.load_from_disk()
        • TDIResult.save_to_disk()
        • TDIResult.select()
        • TDIResult.tcr_adata
        • TDIResult.tcr_df
        • TDIResult.to_pandas_dataframe_cluster_index()
        • TDIResult.to_pandas_dataframe_tcr()
    • Clustering options
      • FAISS_INDEX_BACKEND
        • FAISS_INDEX_BACKEND.FLAT
        • FAISS_INDEX_BACKEND.KMEANS
  • Models
    • get_human_config()
    • TRabModelingBertForPseudoSequence
      • TRabModelingBertForPseudoSequence.forward()
    • TRabModelingBertForVJCDR3
      • TRabModelingBertForVJCDR3.forward()
    • GEXModelingVAE
    • Model options
      • TCR_BERT_ENCODING
        • TCR_BERT_ENCODING.CDR123
        • TCR_BERT_ENCODING.VJCDR3
      • TCR_BERT_POOLING
        • TCR_BERT_POOLING.CLS
        • TCR_BERT_POOLING.MAX
        • TCR_BERT_POOLING.MEAN
        • TCR_BERT_POOLING.POOL
        • TCR_BERT_POOLING.SUM
        • TCR_BERT_POOLING.TRA
        • TCR_BERT_POOLING.TRB
        • TCR_BERT_POOLING.WEIGHTED
  • Training Utilities
    • TRabModelingBertForVJCDR3Trainer
      • TRabModelingBertForVJCDR3Trainer.evaluate()
      • TRabModelingBertForVJCDR3Trainer.fit()
    • TRabTokenizerForVJCDR3
      • TRabTokenizerForVJCDR3.convert_ids_to_tokens()
      • TRabTokenizerForVJCDR3.convert_tokens_to_ids()
      • TRabTokenizerForVJCDR3.to_dataset()
    • TRabCollatorForVJCDR3
  • Plotting
    • set_plotting_params()
    • create_fig()
    • create_subplots()
    • plot_cdr3_sequence()
    • plot_selected_tcrs()
  • Additional Utilities
• Knowledge base
  • Integrating both TCR and GEX information
  • Clustering and similarity search for TCRs
  • Antigen specificity prediction for TCRs
• References