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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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Parser for RTCR #91

Closed vadimnazarov closed 9 months ago

vadimnazarov commented 3 years ago

https://github.com/uubram/RTCR

uubram commented 3 years ago

Dear Vadim,

Thank you for your interest in RTCR! As per your request, see below for an example output file. I'm not sure if it's helpful, but RTCR includes a parser for an older version of your software.

RTCR_output_example.zip

Best wishes, Bram

vadimnazarov commented 3 years ago

Thank you, very helpful!

Oh, I know! But we redesigned and will be redesigning the parsers, so having a "gold standard" output file is extremely important here. This is the reason I asked you personally instead of running the software by myself, because I want to make sure we have this "gold standard", as well as a connection in case of any changes such as major version update. Thank you again!

uubram commented 3 years ago

Dear Vadim,

As of today, the output of RTCR conforms to the Adaptive Immune Receptor Repertoire (AIRR) Community format. Since immunarch supports the AIRR format, it is already able to parse the output of the latest version (0.5.0) of RTCR. You're of course free to also support the output of older versions of RTCR.

Best wishes, Bram

vadimnazarov commented 9 months ago

Closing this issue for now. The next version of Immunarch will mostly support the AIRR Standard data format.

More details on the next version of Immunarch are here: https://b-t.cr/t/immunarch-will-significantly-evolve-but-it-will-break-things-and-we-need-your-help/1123