DoubletFinder for Python?
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Entering edit mode
13 months ago
aerlaut ▴ 10

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?

scanpy doublets scrublet • 1.5k views
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Entering edit mode
13 months ago
Mark ★ 1.5k

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.

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3 months ago
Prakki Rama ★ 2.7k

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

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3 months ago
fracarb8 ★ 1.4k

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

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