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. 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.
The mission of immunarch is to make immune repertoire data analysis as easy and possible - even with R. Please feel free to check it here: https://immunarch.com/
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:
See tcR website for more information, manual and examples: http://imminfo.github.io/tcr/
If you have any questions, suggestions or bug reports, feel free to raise an issue here: https://github.com/imminfo/tcr/issues
The project was developed mainly in the Laboratory of Comparative and Functional Genomics.
tcR internally expects columns with nucleotide and amino acid CDR3 sequences and columns with gene segments to have character class, not factor class. Use
stringsAsFactors=FALSE parameter if you use R functions for parsing files with tables (.csv, .xls and others).
Note for installation on Macs with OSX Yosemite (and potentially other versions): if you receive a compilation error, modify tcR/src/Makvars to: