gravatar for VHahaut

2 hours ago by



I am currently exploring a 10x scRNA dataset. I have defined several short gene sets (+/- 10 genes each) that I see expressed at different levels in specific clusters. For each gene set, I would like to summarise the signature at the cluster level and then compare how much one cluster expresses it compared to another one.

So my two questions can be summarised as:

  1. What approach would you recommend to measure a gene set enrichment in a 10x dataset ?
    I found several tools to do so (fgsea, MAST, AUCell, ...) but was unable to find a benchmarking paper.

  2. How would you compare the results of these enrichments between clusters ?

Thank you in advance !

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