I often use the
GSEA function of the
clusterProfiler package downstream of my differential gene expression analysis. If I understand it correctly,
fgsea under the hood to estimate significance levels and for that, it permutates the gene labels.
However, if I remember correctly, the "original" GSEA implementation (i.e. the one from Subramanian et al.), actually permutates the class labels to preserve gene-gene correlations.
So I was wondering, if there actually is an implementation of the "original" GSEA algorithm that can be called from R. I think the python package
gseapy can do it for example.
Any pointers are much appreciated!