Pathway analysis for mouse gene sets

Question

[iamsmor]

Hello everyone

I have done RNA sequencing analysis for mouse gene sets and now I want to do pathway analysis. I want to use Generally Applicable Gene-set Enrichment tool (GAGE) for those, but I am not sure it is useful and I want to get ideas if it is a good choice or are there better tools for mouse genesets. If anyone has experience with this, I would be grateful to hear from you.

Answer 1

[Ming Tommy Tang]

I have not used GAGE, but this one is very popular https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html