Hello,

I have been trying to use a Java-based tool called BubbleGUM for gene set enrichment that allows multiple comparisons within groups, generally not possible with GSEA. I tried to run for reactome as well as 'all' pathways and I see the same output- some 10 pathways, whereas technically there should be hundreds. Running hallmark on the same gives an error: no gene sets passed the seize threshold.

I have 4 groups in my data: Genotype 1: control, treated Genotype 2: control, treated

If anyone knows about this tool or any other method to visualised pathway enrichment in all 4 groups simultaneously, please let me know!

Thanks, Sonal

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )