differential gene expression analysis comparing different conditions using scRNAseq

Question

[Sara]

I have single cell RNA-seq data (10X genomics) data from PBMC and trying to do differential gene expression analysis comparing different conditions (not comparing different clusters or cell types) per cell type. I am trying to use Seurat R package but I think it only compares clusters to detect markers. using Seurat, is there any way to perform differential gene expression analysis comparing different conditions per cell type? if not, what R package can do this analysis?

[synat.keam]

watch his video on how to analyze and do deg between two conditions. exactly what you need.

Answer 1

[bk11]

You need to perform pseudobulk method for the differential expression that you are planning. Please check out the following methods.

https://hbctraining.github.io/scRNA-seq/lessons/pseudobulk_DESeq2_scrnaseq.html

https://bioconductor.org/packages/devel/bioc/vignettes/glmGamPoi/inst/doc/pseudobulk.html