Single cell clusters annotating to same cell-type

Question

[rykerklie7]

I have KO, WT condition data for which I did an integrative analysis using Seurat. I identified multiple clusters of which some of which annotated to the same cell types, say endothelial cells. What is the best way to see if these clusters are different before pooling them? I have 5 such clusters, should I do the differential expression of one vs others or pseudotime kind of analysis?

[Pratik]

Both sound like a good idea to me. You could subset the data to those 5 clusters temporarily and then do 1 v 5 differential expression analysis and repeat for each respective cluster.

And/or you could do the pseudotime analysis, which I have less experience with, but it does sound like a good idea. You labeled Monocle, so you could use that. I've also seen people use slingshot (bioconductor package), and then you could extract the gene clusters, i beleive. If you're interested in using slingshot, I could tag someone who might be able to help.