I need some help regarding differential expression (DE) in single cell RNA-seq data between two biological samples.
Here is the situation: I have two biological samples (you can consider these two samples as two different datasets where one is a disease case and another is control). We sequenced these two samples using single cell protocols and identified around 7000 cells in each of the samples. We have done cell identification and differentiation within each of the samples. Now we would like to see if we can find genes that behaves differently in these two samples.
I know, there are methods/packages that do the DE between cell clusters, but couldn't find any that what I'm looking for. I would really appreciate any idea/suggestion.