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ncborcherding / scRepertoire

A toolkit for single-cell immune profiling
https://www.borch.dev/uploads/screpertoire/
MIT License
306 stars 52 forks source link

Predict the antigens? #291

Closed mainyanghr closed 10 months ago

mainyanghr commented 10 months ago

This is a great package, I am wondering whether we could predict the antigens or any other packages are recommended for antigen prediction?

Thank you very much!

ncborcherding commented 10 months ago

There is no ideal epitope prediction pipeline for TCRs. scRepertoire does not have prediction capabilities, but there is Trex (compatible with scRepertoire), which could be used for unsupervised epitope discovery/prediction.

Other pipelines you might want to check out:

Just a not - this area is exploding right now with tools and publications. There are a ton of alternative to the above. Best practice is probably combining several and looking at the intersection.

Hope that helps, Nick

mainyanghr commented 10 months ago

Thank you very much for great response. You are the best!

Have a nice day! Looking forward to collaborate with you.