Hi everyone,
I am trying to analyse some mRNA-Seq data that I have generated using GSEA.
I am able to generate the data using the GSEA application, but I was wondering if there was a method to carry out the traditional GSEA in R, to streamline the analysis/data presentation. It appears that most of the packages for GSEA that I have found are more similar to GSEA Preranked, which I would prefer not to use because it sounds like GSEA is better for permutations (https://groups.google.com/g/gsea-help/c/BE5H_GUuMkE).
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james.zhang20 •
I've used fgsea with a lot of success. https://bioconductor.org/packages/release/bioc/html/fgsea.html
This is technically preranked, but ranked using information from differential gene expression analysis. Not sure where your hangups are with preranked GSEA, so I'd like to hear more about your concerns there.
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
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