DoubletFinder for Python?

Question

[aerlaut]

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?

Answer 1

[Mark]

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.

Answer 2

[Prakki Rama]

You can check single cell best practices on how to use scDblFinder to remove doublets in anndata object using scanpy.

Answer 3

[fracarb8]

scvi-tools uses SOLO for doublet detection. You find the paper here.