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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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Support for file format Qiagen Immune Repertoire Analysis #232

Closed ElviMagda closed 2 years ago

ElviMagda commented 2 years ago

Dear Immunarch team,

We started to use the QIAseq Immune Repertoire kit from Qiagen for our bulk TCR sequencing. For the data processing, we used the module of the Qiagen CLC workbench. The output table looks like this:

image https://resources.qiagenbioinformatics.com/manuals/biomedicalgenomicsanalysis/current/index.php?manual=Immune_Repertoire_Analysis.html

I would like to analyse the data with your very nice package :) Is there a possibility to implement this file format, please? Thanks in advance!

Best, Elvira

ElviMagda commented 2 years ago

Hi,

we were able to export the data in the VDJ tool format with the CLC workbench and use it in the Immunarch package. So I think there is no need to implement the other format :)

Thanks anyway! Best, Elvira

Alexander230 commented 2 years ago

Hi, Elvira!

I'm glad to hear that you've resolved the problem. Thank you for the instructions how to load the data from QIAseq to Immunarch!

Best regards, Aleksandr Popov