The original question was GSEApy vs KEGG. The response below is GSEApy. The question has been edited and is now a different question concerning options within GSEApy.
Response to original question
If GSEApy as described in the publication provides the output you require – that is much, much simpler. KEGG will be complex and you’d need its ids.
However, surely GSEA will require to perform the full calculation of fold-change from scratch rather than be fed the output of scanpy? KEGG will require the output of scanpy. GSEApy primary function is fold-change rather identifying the precisely which pathways are regulating the phenotype under analysis.
KEGG will provide a more accurate answer – in my humble opinion. GSEApy is a lot easier because it very much an “all-in-one” solution. If the answer isn’t satisfactory you can always switch.
Just to note the GSEApy version I’m referring to is the latest publication.
NOTE There was a deleted post from the OP about an option within GSEA. This is a separate question in the SE format of questions and answers. Thats the way the site works.
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