I'm currently working on a functional analysis of RNAseq data. I've used the GSEA tool by the Broad Institute to obtain quick results and now I'm trying to reproduce the results with R for visualization purposes.
The fgsea is amazingly fast but apparently there is no way to calculate a weighted enrichment statistic which is why my results differ from the original analysis with the GSEA tool. Then I've looked at the DOSE tool as this allows for a weighted enrichment statistic. However, here I can't use the MSigDatabase gene set collection. ClusterProfiler doesn't seem to provide a GSEA preranked option.
Did I miss a function of these packages that would allow me for a GSEA on a preranked list with the MSigDatabase gene set collection and at the same time gives me the option to calculate a weighted enrichment statistic? Is there any other way to solve this problem?
Thank you very much for help in advance!!