I have different gene lists from different biopsies. In each gene list, all genes are listed which carry a mutation (identified by WES). I want to run a overrepresentation analysis, to check if certain pathways are more hit by mutations than others. However, for many gene lists there is the same gene listed multiple times, because there happened to be more than one mutation in that gene. By default the ORA tool I am using (webgestalt) removes duplicated genes, however, I think in my case it might be useful to keep them.
I am very new to ORA/GSEA, so I am not sure if this makes sense. Furthermore, I did not find a tool yet, which allows me to keep duplicated genes. If somebody could tell me if my idea makes sense and also a tool or a way how I can analyze the gene lists, I would be very happy!