Corelate TCR data to clusters/GEX/CITEseq data · Biostar

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Corelate TCR data to clusters/GEX/CITEseq data

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

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updated 5.0 years ago by theHumanBorch •

• written 5.1 years ago by chi.delta •

1 answer

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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written 5.0 years ago by theHumanBorch •

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