vadimnazarov
commented
5 years ago Hi, 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 the 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/
If you have any suggestions, bugs, improvements, etc. -- please write us or create an issue in https://github.com/immunomind/immunarch/issues
Thank you! Sincerely, immunarch dev team and Vadim I. Nazarov, lead developer
Hello
I just noticed a strange absence in the set of V gene segments (the HUMAN_TRBV vector): it seems that the TRBV6-8 and TRBV6-9
( two gene segments coding those specific T-cell receptor beta variable) are not present. Since they are both functional, why to exclude them from the whole set?
It seems these two are the only non pseudo-genes which are currently missing.
Could you please explain the rationale behind your choice? It is a pity because, as you can imagine, the whole statistical analysis will suffer from this lack
cheers