Importing KEGG pathways into cytoscape
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4.4 years ago
support ▴ 40

I installed cytoscape, and install the KEGGScape app for it. So I imported the KGML file for the citric acid cycle pathway. Heres what came up in cytoscape:

enter image description here

Completely incomprehensible. Its supposed to look something more like this: enter image description here

When I click the Apps menu, KEGGScape is the only installed app that doesn't show up in the menu. If I go into the app list, it lists keggscape as installed. I'm using cytoscape 3.4.0. Is this a problem with KEGGScape?

cytoscape kegg keggscape • 1.8k views
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3 months ago
Dr SKY ▴ 20

Hello, I found you finally. I am going through the same prob....haha

If you have found the way out. Please let me know Thanks in advance

However, you may use cytoKEGG plugin to import the same...This initially gives you the exact image like in KEGG but the prob that even i am facing is that its gets transformed into circles like your first diagram whenevr i am tring to modify it using the STYLE column or saving it as a network. 3 tools to import and viaualise KEGG are KEGGscape cytoKEGG KEGGparser

Regards Akash D

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