search

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
31 stars 12 forks source link

No longer able to create an enrichment map with just a gmt file #473

Closed risserlin closed 2 years ago

risserlin commented 2 years ago

Not sure when this functionality disappeared but if you just specify a gmt file a enrichment should be built but it now comes up with an error saying missing an enrichment file. If you get rid of the dataset and just specify the gmt file the build button is disabled.

mikekucera commented 2 years ago

Hi Ruth, I just tested this with EnrichmentMap 3.3.3 and a baderlab GMT file and it works. I was able to create an enrichment map network with just the GMT file.

Perhaps the issue is specific to C2 pathways from Msigdb?

Can you please send me the file you were using when you ran into this error?

Thanks.

risserlin commented 2 years ago

HI Mike, You are right. It does work. I think that I tried to create it by specifying just gmt file in the common files section. If you add a dataset and add the gmt to the dataset it works. Thanks, Ruth