I am analyzing snRNA-seq data that is composed of a KO and WT sample. I have integrated/anchored and clustered the two datasets to identify similarities and differences across the two samples. I have identified the DEGs for each cluster of each sample independently using FindMarkers... But beyond this we would like to generate a list of DEGs for each cluster that compares the KO and WT in order to identify the differences our KO is causing. Is there a function to specifically look at DEGs between samples in specific clusters?
Thank you for your help.