Could your team plant to update SoupX for Seurat_v3.0 ?

constantAmateur / SoupX

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

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Could your team plant to update SoupX for Seurat_v3.0 ? #10

Closed Suzuk1 closed 5 years ago

Suzuk1 commented 5 years ago

Hi,

I am using SoupX for my 10X data and it seems to be nice for reducing soup !

Recently, Seurat_v3.0 was pre-released accompanied with big upgrading of 10xCellRanger. Seurat_v3.0：https://satijalab.org/seurat/ CellRanger3.0：https://www.10xgenomics.com/solutions/single-cell/

I want to use SoupX with Seurat_v3.0 .But I can not use new 10x data in SoupX now. Could your team plant to update SoupX for Seurat_v3.0 ?

Best regards,

constantAmateur commented 5 years ago

The latest update to the package should allow you to load cellranger v3 output with the load10X function as before. I'm not really sure what you are referring to with Seurat V3. The output of SoupX is a corrected sparse matrix which can be loaded into any downstream analysis package, including any version of Seurat, instead of the uncorrected input.