Hi Biostars community, I'm doing a project to read-in patient RNA-Seq raw data and to ultimately search for possible pharmaceutical targets for certain types for cancers. I have posted before in utilizing GSEA and DEG together, but have gotten mixed responses, and I am currently thinking to only use DEG right now since utilizing GSEA and DEG together seem to be a difficult task, but I've ran into pathway analysis and was wondering if this would be appropriate to use.
I've never done pathway analysis (read https://advaitabio.com/news/pathway-analysis-vs-gene-set-analysis/ for differences between pathway analysis and gene set analysis (the latter is DEG, GSEA, etc), so if anyone who have experience in doing this, please let me know how I can implement packages in R that perform pathway analysis (ex. Rontotools) and analyze output data.
Thank you so much :)