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imminfo / tcr

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.
https://immunarch.com/
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Monkey TCR support #34

Closed charlesliu1975 closed 8 years ago

charlesliu1975 commented 8 years ago

Does tcR support monkey TCR？ I found segments.alphabets support human and mouse only. Could you please add monkey TCR. There are 59 TRBV and 13 TRBJ genes of monkey in IMGT.

Can I analyse the IMGT results?

Thank you.

vadimnazarov commented 8 years ago 
Does tcR support monkey TCR？ I found segments.alphabets support human and mouse only. 
Could you please add monkey TCR. There are 59 TRBV and 13 TRBJ genes of monkey in IMGT.

Hi, sure, done. You need to update to the latest development version from GitHub. Name of gene alphabets - MACMUL_TRBV and MACMUL_TRBJ

# install.packages("devtools")
devtools::install_github("imminfo/tcr", build_vignettes = FALSE)

Please let me know if it works (or not) for you.

Can I analyse the IMGT results?

I'm sorry, but no, you can't analyse the IMGT results with the package. I highly recommend you to use MiXCR or MiGEC. It's been shown that MiXCR and MiGEC allows more precise and faster identification of TCR / Ig gene segments. For those tools I have a parsers of their outputs in the package.

vadimnazarov commented 8 years ago

Added rhesus monkey alphabets.