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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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DAVID/BINGO/Great import gives error "Enrichments file or GMT file is required" #447

Closed kjbussey closed 3 years ago

kjbussey commented 3 years ago

I am trying to use EnrichmentMap to visualize the Functional Annotation Chart from a DAVID analysis. To make sure that the tool worked, I attempted to load the 12hr_David_Output.txt that you provide as a demo file and received the error: "Enrichments file or GMT file is required." I was under the impression that for DAVID, this file was optional, so this looks like a bug. I'm using version 3.3.1 with Cytoscape version 3.8.2 with Java 11.0.6 by AdoptOpenJDK on Windows 10, version 1909, 64-bit on a machine with 64 GB of RAM.

EnrichmentMapApp_bugreport.zip

risserlin commented 3 years ago

You are correct. With DAVID results you should not be required to specify anything besides the output file. I am not able to recreate this issue though.
When I use the file you supplied I get no error and I get the following EM:

Screen Shot 2021-02-17 at 9 05 53 AM

When you try to create an EM with your David file is the analysis type set to "David/Bingo/great" ?

kjbussey commented 3 years ago

Yes. However, in testing today after re-booting the computer and re-starting Cytoscape, it loaded fine. Not quite sure what is going on there.

Kimberly J. Bussey, Ph.D.

Managing Partner, Equinox Technologies, LLC

Assistant Professor, Precision Medicine, Midwestern University

Adjunct Faculty, Mathematical and Natural Sciences, The New College, ASU

Adjunct Faculty, The BEYOND Center for Fundamental Concepts in Science, ASU

Email: mailto:kjbusseyphd@gmail.com kjbusseyphd@gmail.com

Phone: 480-321-7137

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From: Ruth Isserlin notifications@github.com Sent: Wednesday, February 17, 2021 7:09 AM To: BaderLab/EnrichmentMapApp EnrichmentMapApp@noreply.github.com Cc: Kimberly J. Bussey, Ph.D. kjbusseyphd@gmail.com; Author author@noreply.github.com Subject: Re: [BaderLab/EnrichmentMapApp] DAVID/BINGO/Great import gives error "Enrichments file or GMT file is required" (#447)

You are correct. With DAVID results you should not be required to specify anything besides the output file. I am not able to recreate this issue though. When I use the file you supplied I get no error and I get the following EM: https://user-images.githubusercontent.com/3842763/108215506-66e22480-70ff-11eb-9cf3-7ea46daf29d1.png

When you try to create an EM with your David file is the analysis type set to "David/Bingo/great" ?

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