Corelate TCR data to clusters/GEX/CITEseq data
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2.7 years ago
chi.delta ▴ 40

Hello everyone,

I just added my TCR VDJ data as metadata to my Seurat object (as described in the tutorial here). So, I basically ended up with two different collumns of metadata where my barcodes are assigned to the clonotypes and the cdr3 sequences. As a next step I would like to correlate my clonotypes to certain features of my gene expression or my Cite seq data. Or for example check the frequency of a certain clonotype within each of my umap clusters.

Does anyone have in mind any way or package that would help me with this approach?

Thanks a lot in advance

10x vdj tcr seurat • 986 views
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Entering edit mode
2.6 years ago
theHumanBorch ▴ 240

What is the method you are thinking for correlation? I am the author of scRepertoire and would be interested to know what exactly you're thinking and if I can incorporate the idea into the package to make it easier for everyone. As an aside - there is a huge overlap in terms of feature space and clones, clonality seems to be a large predictor of cluster, so I think this is a very interesting space to look at.

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