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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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geneset not found in gmt file #369

Closed whitleyo closed 5 years ago

whitleyo commented 5 years ago

Hi,

I'm getting an error saying that a geneset is not found in a gmt file when in fact it is in the provided gmt file. This happens when I use the generic/gprofiler mode for loading data into EnrichmentMap and provide appropriate inputs. This doesn't happen when I use GSEA generated enrichment results under the 'GSEA' mode for loading data, and in this case the exact same gmt file is provided.

Here's the error.

image

And here's a screenshot of the gmt file:

image

Cytoscape Version 3.7.0, Enrichment Map version 3.1.0 installed.

whitleyo commented 5 years ago

Issue was with file formatting for gmt. downloading gmt files from https://biit.cs.ut.ee/gprofiler/static/gprofiler_mmusculus.name.zip and using the GOBP gmt file solved the issue.