Comparing DEG lists between clusters, looking for unique/differences in pathways between them

Question

[Michael]

Hi all,

I'm looking for the best way to approach a question regarding DEGs.

I have 2 conditions (stim/unstim), and have made DEG lists of each of the 3 different clusters between the conditions.

My cell types are very similar though, just really specific types of certain cells. So what i'm looking to do is now compare the DEG lists between each other in order to find differences between them. Basically i'd like to ask, between clusters, are there different pathways are upregulated more in the stimulated condition, compared to another cluster.

I'm currently trying to use gProfiler and stringDB to look a the pathways/gene ontologies and try and get an idea of what pathways are different, but i'm looking for a more statistical way to go about this, or something that is visually helpful.

Any thoughts? hopefully this makes sense. My googling is just showing up how to make DEG lists, but i'd like to go one step further and compare the DEG lists.

[jv]

what about GSVA for R? https://www.bioconductor.org/packages/release/bioc/html/GSVA.html

[Michael]

Thank you! this looks pretty close to what I need, but i'm having difficulty preparing my single cell data for this (looks like it was made for bulk RNA seq?). I did some searching and got directed towards cerebro, but that doesn't seem to be working either (and is no longer in development).

anyone with ideas?