Hey everyone!

I'm currently working on a project where I performed bulk RNA seq of vehicle-treated and two time-point treated rat stem cells (EG. A, B, C), which so far, seems to show that they are transitioning out of their stem cell status and activating.

There is a LOT of single-cell RNA seq data out there of my cells of interest and folks have already done a nice analysis of the lineage trajectory decisions points and have identified various sub-populations of my cells of interest in vivo (mouse + human available).

What I'd like to do: I'd like to compare my data set containing 3 subpopulations of my stem cells and use the single-cell RNA seq in vivo data to determine "where" my cells are located across this temporal landscape of activation. Something like a pseudotime? The single cell RNA seq paper did a fantastic job of identifying gene signatures for the various states of my stem cells. My initial plan to carry out GSEA analysis. However, I have some reservations because GSEA could only do Vehicle vs. TimePointA and/or Vehicle vs. TimePointB.

Does anyone have any suggestions or papers for how to perhaps do this; or are there multivariate GSEA tools that can take a gene set that I input and assess enrichment across multiple groups?

Thank you!