Here we provide scripts and commands we used in our study "Rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing".
Table of contents
We have used following RNA-Seq based TCR profiling tools:
- MIXCR (v 3.0.13), https://mixcr.readthedocs.io/en/master
- IMREP (v 1.0), https://github.com/Mangul-Lab-USC/ImReP
- TRUST4 (v 1.0.2), https://github.com/liulab-dfci/TRUST4
- CATT (v 1.9.1), https://github.com/GuoBioinfoLab/CATT
This study used 19 samples which were sequenced by both TCR-Seq and RNA-Seq. The data included in this repository contains the results of the methods, as well as the processed TCR-Seq data.
summary_data includes the data that created all figures in the manuscript.
notebooks includes the Jupyter notebooks for all figures in the manuscript.
figures includes all of the image files for the plots generated by notebooks.
Please do not hesitate to contact us ([email protected]) if you have any comments, suggestions, or clarification requests regarding the study or if you would like to contribute to this resource.