Question: Has anyone used R package "RontoTools" for pathway analysis before? Am I using this for the correct purpose?
gravatar for chokevin8
6 months ago by
chokevin80 wrote:

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 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 :)

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