Hi Scanpy Discourse,
I am finishing up some DGE analysis on my scRNA data, but my team is very interested in seeing DGE between two groups irrespective of the cluster.
Currently, I run rank_gene_groups to retrieve differential expression analysis per cluster for each group. What I would like to know if is it possible to run the differential expression analysis for two groups with all expression data in one set, instead of per cluster.
Please let know if you have any experience or insights!