Hi all, I have a single-cell data set which I have analyzed via Seurat. All clusters have been annotated. Now my aim is to look at GO term enrichment differences across each sample for every cluster. I.e.: if I have a cluster for neutrophils, what are the pathways enriched for sample 1 vs. sample 2 and what are the genes represented in each enriched pathway.
I know this requires a Pseudobulk analysis, but I am not sure what would be the best way to approach this. And once I convert the data to pseudobulk, what pathway analysis package would take the pseudobulk data?