Hi excuse me for any ignorance, I’m not sure if what I’m asking is very simple or difficult to perform. What I currently have in my work is a set of genes of interest which express a specific pattern in my cells when plotted using UMAP. (All genes in set show mostly the same cells expressing them.) What I would like to know is, for the cells expressing this genes from this set, what other genes are expressed most highly?
If possible it would be nice to perform a gene ranking for these cells compared to all others. I struggled to figure out how to perform this… I could imagine saving cells which express any of these genes as their own observation and then performing gene ranking this way, but I am unsure what commands to run to do this, or if there is another built in method which would be better to use. What would you recommend in order to do this?
Thanks so much in advance and I would be happy to clarify if anything is confusing about this request.