Ruth Isserlin

I am getting the same error. I am using the package with python 2.7 because of other dependencies. I rolled back to using a previous version of goatools because I...

here is the header row for fGSEA results that I have created - name description GS details SIZE ES NES pval padj FWER Rank at Max leading edge genes (truthfully...

Hi Lena, It is unclear what you are using for a ranked file in your GSEA analysis. I looked through the documentation for clusterProfiler but I can't find descriptions of...

Hi Lena, I usually separate into up or down lists when I do thresholded analysis using g:profiler (or other thresholded methods). Are you using GSEA java desktop app or are...

I don't think this is the issue because when I run your code I get a different error. The method should be "ssgsea" not "gssea" Is your data a seurat...

Can you send me a sample of the output files for fgsea (just the top two or three lines of the file will be sufficient).

Initial method - the format of the files that are coming out of fGSEA are not the same as the regular GSEA files. I would recommend converting them to generic...

for your fgsea results to mimic GSEA results they need to have the following columns. Your current output format is not a recognized format for EM NAME description GS DETAILS...

@veroniquevoisin would like to keep the node size to reflect the size of the post analysis set including the genes that are not in any dataset so the user can...

This wouldn't be needed, I think, if what was being searched for is transparent. If #481 was implemented I think this would be solved.