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SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
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SingleR and FindAllMarkers with Seurat Object using SCTransform v2 #225

Closed Chris-lang478 closed 1 year ago

Chris-lang478 commented 2 years ago

Hi Christoph, I appreciate all your work. I have a question related to SingleR and Seurat objects.

I integrated two datasets using CCA-based method after scTransform normalization. The discussion in https://github.com/LTLA/SingleR/issues/98 is great to learn. In previous SCTransform，the team recomand to use raw counts with singleR and FindMarkers(https://github.com/satijalab/seurat/discussions/5605).

I read the paper for scTransform v2, With the release of SCTransform v2 ,the team recommend using the RNA or SCT assay ("data" slot) for performing DE.(https://satijalab.org/seurat/articles/sctransform_v2_vignette.html)

Is it right to use SCT assay produced by SCT v2 performing the cells annotations with singleR?Is there any more documentation about this?

In my cases I am integrating two samples from same tissues with different treatments to compare cell types between them.

Thanks!

LTLA commented 2 years ago

I dunno who Christoph is, but see #98.