I'm trying to process s single-cell RNA seq data using Scanpy. I usually use Seurat.
One of the major difference when using Scanpy is the lack of scDoubletFinder. The recommended alternative is to use scrublet. However, I find a large difference between the result of scrublet and scDoubletFinder.
Are there better alternatives to scrublet? Will scDoubletFinder be implemented in Python?
3 answers
There are a few tools that can detect doublets. There's souporcell https://github.com/wheaton5/souporcell and veiro https://github.com/single-cell-genetics/vireo that I know of.
The souporcell paper is a very good read and includes other packages.
You can check single cell best practices on how to use scDblFinder to remove doublets in anndata object using scanpy.
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