TCRconvert

Convert TCR gene names

TCRconvert converts V, D, J, and/or C gene names between the 10X Genomics, Adaptive Biotechnologies, and IMGT nomenclatures. IMGT is the AIRR Community–recommended standard. TCRconvert supports alpha-beta and gamma-delta T cell receptors (TCRs) for human, mouse, and rhesus macaque. Users can also define custom species (see the docs). An R version is also available.

Use TCRconvert as a Python library or on the command line.

Contents:

• Installation
• Library: Quick Start
• Library: Custom Species
• Command-line: Quick Start
• Command-line: Custom Species
• FAQ
• Functions
• Contributing

Background

TCR annotation tools use different gene naming conventions, making cross-dataset searches difficult (e.g., identifying 10X-annotated TCRs in Adaptive data). Manual conversion is complex and error-prone due to inconsistencies in naming rules.

TCRconvert automates this process efficiently and accurately. Our approach is based on analyzing multiple 10X and Adaptive data sets to capture their naming variations.

Issues

To report a bug or request a feature please open an issue.

Contact

For other inquiries, contact Emma Bishop: emmab5 at uw dot edu.

Acknowledgments

This project was supported by the Fred Hutchinson Cancer Center Translational Data Science Integrated Research Center (TDS IRC) through the 2024 Data Scientist Collaboration Grant. Special thanks to Scott Chamberlain for development support and Shashidhar Ravishankar for gene name curation.