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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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GSEAtutorial.zip not working with EnrichmentMap #471

Closed ARW-UBT closed 2 years ago

ARW-UBT commented 2 years ago

Hello, I have tried to use the data in GSEAtutorial.zip (https://enrichmentmap.readthedocs.io/en/latest/_downloads/419eb265cf06a982bb39816dbccdcc8a/GSEATutorial.zip) to run GSEA in the Cytoscape app. Unfortunately, the 'scan folder for enrichment data' in the app seems not to work with these data.

According to the quick tutorial at readthedocs, it should contain all data for GSEA, or did I get it wrong? To be more specific: I do have a ranked list and a gmt file, which I want to sunmit to GSEA.

Thanks for your suggestions.

risserlin commented 2 years ago

Are you trying to run GSEA from cytoscape? If you have a rank file and a gmt file then you first need to run it in GSEA to get the results that EM in Cytoscape can use.

ARW-UBT commented 2 years ago

Thanks for the fast reply and the clarification. I have seen that GSEA can hand over the results directly to a Cytoscape instance. Best regards,