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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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parsing mixcr 3.0.3 file #101

Closed ekelley903 closed 5 years ago

ekelley903 commented 5 years ago

Hello,

It looks like the latest mixcr release, 3.0.3, is no longer parseable by tcR. The clonotype counts were previously an integer, but are now a float and this is producing an error.

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'an integer', got '4347.0'

tiagobrc commented 5 years ago

Same problem here. Do you have a solution?

Thanks.

ekelley903 commented 5 years ago

I dropped the analysis w/ tcR at this point, because it looked to me like the package is no longer being supported. You might try converting the float to an integer prior to parsing w/ tcR.

tiagobrc commented 5 years ago

Thanks for the help. It is a good short term solution.

Thanks!

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 new package “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