Hi,
Is there a way to analyze the VDJ regions that T cell falls into using the scRNA data? R package is preferable.
I'm working on TCR data from RNA (not scRNA) but MiXCR did a great job on identifying VDJ regions and VDJtools works well for R plotting.
Hope this helps and would love to learn along with this question.
MiXCR: https://mixcr.readthedocs.io/en/master/index.html
VDJtools: https://vdjtools-doc.readthedocs.io/en/master/
I think you could try this:
doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13.. 2021 Jun;18(6):627-630.Nat Methods
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data
Li Song 1 2, David Cohen 1, Zhangyi Ouyang 3, Yang Cao 4, Xihao Hu 1 2, X Shirley Liu 5 6 7
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