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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Is there any way to extract gene names that have deletions from infercnv analysis? #639

Open mbihie opened 7 months ago

mbihie commented 7 months ago

I am looking to highlight the genes associated with copy number deletion. I was able to run the full analysis and I have heat maps with deletion present, but how would I extract the gene names from the output?

shubham-koirala commented 6 months ago

Hey @mbihie were you able to figure it out? I am willing to highlight CNV gain and loss in particular chr for particular cell types.

tianaoch commented 6 months ago

We provide a gene expression matrix, but in the output, there are some gene deletions relative to this gene expression matrix. So What can we do with it? What does it mean to be missing