[Question] Using soupX together with doublet detection tools

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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[Question] Using soupX together with doublet detection tools #24

Closed JonathanCruard closed 4 years ago

JonathanCruard commented 4 years ago

Hi, thanks for this great tool.

I'm testing various tools dedicated to scRNAseq data and I was wondering if you have any idea of the impact of soupX on the performance of doublet detection tools.

Thank you in advance. JonathanCruard

constantAmateur commented 4 years ago

This is a good question that I haven't systematically investigated. For now I'd recommend running your doublet detection first, getting a list of non-doubleted cells, then loading them using SoupChannel directly as per this issue.

Xyanhong commented 8 months ago

Interestingly, doublet detection methods like doublet finder requires an cleaned-up input for low-quaility data