Awesome

tcR

The tcR package is no longer supported and current issues will not be fixed.

A new package is available that is designed to replace tcR called immunarch: https://immunarch.com/

We have solved most of the problems tcR package had and improved the overall pipeline, providing functions for painless repertoire file parsing and publication-ready plot making. We will be happy to help you to integrate the new package into your pipelines. Please do not hesitate to contact us via emails on https://immunarch.com/ or via issues on https://github.com/immunomind/immunarch, should any question arise.

Sincerely, immunarch dev team and Vadim I. Nazarov, lead developer

tcR is a platform designed for TCR and Ig repertoire data analysis in R after preprocessing data with software tools for CDR3 extraction and gene segments aligning (MiTCR, MiXCR, MiGEC, ImmunoSEQ, IMSEQ, etc.). With the power and flexibility of R language and procedures supported by tcR users can perform advanced statistical analysis of TCR and Ig repertoires. The package was published in BMC Bioinformatics, please cite if you use it:

Nazarov et al., tcR: an R package for T cell receptor repertoire advanced data analysis

The project was developed mainly in the Laboratory of Comparative and Functional Genomics.