TCR2HLA Tools and Databases

This repository provides tools and resources for analyzing T-Cell Receptor (TCR) repertoires in relation to Human Leukocyte Antigen (HLA) proteins. It includes functionalities for HLA imputation from TCR repertoire data and for querying a database of TCR-associated alleles.

Preprint

For a detailed description of the methods and data presented in this repository, please refer to our preprint:

Decoding the restriction of T cell receptors to human leukocyte antigen alleles using statistical learning

Overview

This repository is structured as follows:

• /CLI_tools/impute_HLA: Contains the impute_HLAs tool for imputing HLA alleles from TCR repertoire data.
• /CLI_tools/query_database: Contains the query_database tool for interfacing with a database of HLA-associated TCR clonotypes.
• /databases: Stores various databases, including TRA and TRB clonotypes strongly associated with specific HLA proteins.
• /models: Stores the models and the weights for imputing HLA alleles from TCR repertoire informations.
• test_dataset.tsv: A test TRB repertoire derived from the immuneCODE database. This dataset can be used to check the installation and test the functionality of the provided code.
• requirements.txt: Lists the necessary Python packages for running the tools.

Tools

We provide two primary tools, each available as both a command-line interface (CLI) and a programmable API:

1. impute_HLAs (HLA Imputation from TCR Repertoire)

This tool allows users to predict HLA alleles based on their TCR repertoire data.

• Functionality: Imputes HLA from TCR repertoire.
• Location: /CLI_tools/impute_HLA/
• Usage:
  • Command Line: Detailed usage instructions can be found in /CLI_tools/impute_HLA/README.md.
  • Programmable Interface (API): For scripting and integration into other Python projects, refer to the documentation within the /CLI_tools/impute_HLA/ directory.

2. query_database (TCR-HLA Database Interface)

This tool enables users to query our curated database of HLA-associated alleles.

• Functionality: Queries a database of HLA-associated alleles.
• Location: /CLI_tools/query_database/
• Usage:
  • Command Line: Detailed usage instructions can be found in /CLI_tools/query_database/README.md.
  • Programmable Interface (API): For scripting and integration into other Python projects, refer to the documentation within the /CLI_tools/query_database/ directory.

Databases

The /databases directory contains valuable resources, including:

• TRA and TRB clonotypes: These files contain TCR Alpha (TRA) and TCR Beta (TRB) clonotypes that have been identified as strongly associated with specific HLA proteins.
• adaptive_imgt_mapping.tsv: This file provides a mapping between Adaptive Biotechnologies' nomenclature and IMGT (International Immunogenetics Information System) standard nomenclature for TCR gene names. The file is obtained from the tcrdist3 tool.

Installation

To set up the project and install the required dependencies, follow these steps:

1. Clone the repository:

   git clone https://github.com/ikmb/TCR2HLA.git
   cd TCR2HLA

2. Install dependencies: Ensure you have pip installed. Then, install the packages listed in requirements.txt:

   pip install -r requirements.txt

Contributing

We welcome contributions! Please see CONTRIBUTING.md for guidelines on how to contribute to this project.

Contact

For any questions or issues, please open an issue on the GitHub repository or contact h.elabd@ikmb.uni-kiel.de.