.. tcr-converter documentation master file, created by sphinx-quickstart on Tue May 14 12:36:14 2024. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. 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. .. toctree:: :maxdepth: 1 :caption: Contents: installation usage_library custom_species_lib usage_cli custom_species_cli 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.