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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
296 stars 65 forks source link

Other supported formats #167

Open robwatson15 opened 2 years ago

robwatson15 commented 2 years ago

Hi, can immunarch read in repertoire data that has been outputted from the CLC Workbench from Qiagen (https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-clc-main-workbench/)? Repertoire data is outputted in the format of .txt files which should be relatively straightforward to parse. I've attached an example of the data here (5 rows = 5 TCR chains). Many thanks for your help. example_rep.txt

dstcr commented 2 years ago

I have a similar request!

Alexander230 commented 2 years ago

Hello @robwatson15 and @dsrai,

Thank you for contacting us!

At the moment there is no such parser present in the Immunarch. We will most certainly keep your wish in mind as a feature to improve the package in the near future.

The simplest way for you is to rename the columns in accordance with the AIRR format: https://docs.airr-community.org/en/stable/datarep/rearrangements.html; here is an example of file in this format: https://github.com/cran/airr/blob/master/inst/extdata/rearrangement-example.tsv.gz?raw=true.

I will get back to you with any updates.

Thank you so much for drawing our attention to this. Do not hesitate to contact us with any questions further along.

Best regards, Aleksandr