Question: Any recommendations for copy number variation (CNV) packages for scRNA-seq?
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gravatar for jrleary
10 months ago by
jrleary130
Lineberger Comprehensive Cancer Center
jrleary130 wrote:

A paper I read recently mentioned in the methods that the authors performed copy number variation analysis on their single cell data, but neglected to mention the software used to perform the analysis. I've looked around and seen a lot of desktop and web-based tools, but few for R and few that specifically mention single cell RNAseq. Preferably, I'd be able to integrate this analysis into my downstream analysis R pipeline, but Python tools are fine too.

single cell cnv scrnaseq R • 826 views
ADD COMMENTlink modified 10 months ago by jared.andrews078.0k • written 10 months ago by jrleary130
1

A few options are mentioned in a previous thread: Detecting copy number alterations based on RNA-seq data

ADD REPLYlink written 10 months ago by igor11k
2
gravatar for jared.andrews07
10 months ago by
jared.andrews078.0k
Memphis, TN
jared.andrews078.0k wrote:

inferCNV or CONICSmat are probably the easiest to just pick up and try. It's important to remember that scRNA-seq data is sparse though, and you're not going to pickup small focal changes or get the high-resolution that you would with WGS or exome. It works better if you already have a list of CNAs from bulk WGS or such to feed in. You can, however, usually pick up changes in highly clonal cell populations fairly well. Certainly well enough to be of use.

ADD COMMENTlink written 10 months ago by jared.andrews078.0k
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