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navinlabcode / copykit

Toolkit for single-cell copy number analysis
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application of CopyKit #95

Closed veramazzara closed 1 year ago

veramazzara commented 1 year ago

Dear Darlan, thank you for this very exciting tool!

I am wondering if it possible to apply CopyKit on scRNAseq instead of scDNAseq?

Regards,

Vera

darlanminussi commented 1 year ago

Hi Vera,

If you mean use CopyKit for results of copy number inferences from CopyKat or InferCNV, that is doable but untested. It probably works best with CopyKat since they share similarity of the scaffold.

If your intention is for the analysis of scRNASeq datasets CopyKit is not the right tool for it and there are much better tools such as SingleCellExperiment framework or Seurat that are made for this purpose.

Best