Im very new to Scanpy so i apologise if this is a simple question.
I have carried out ‘leiden’ clustering and visualised this all very nicely. I have also made some dot plots of specific genes over my different clusters
However, what i would now like to do, instead of looking for the differentially expressed genes between the clusters, is to look to see if a certain set of genes are differentially expressed (and get p values etc). I have tried to use the sc.tl.rank_genes_groups command for this but it seems this just gives me the top ranked, and i cannot specify a specific gene set…I have had a look around the scanpy literature, but i cant seem to find anything on this…
Is there a solution to this?
Any help would be very much appreciated!
Thanks in advance,
A very new Python/Scanpy user