Dear All,

I am wondering whether I can use DESeq2 to perform PCA for sample/group clustering using DESeq2 package from 10X single cell data. If possible, could you guide me to the tutorial to perform it. I have single data from 10X genomic (9 samples split into 3 groups). I would like to do PCA whether these three groups are separated from one another. Hope you could help!

Kind Regards,

Synat

DESeq2 PCA is basically just the stats function prcomp() with some extras. Yes, you could use that, or better, follow the best practices for single-cell analysis from Bioconductor:

https://bioconductor.org/books/release/OSCA/