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Questions tagged [cytoscape]

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Edge table on cytoscape won't show gene name on the shared name pp interaction column

Could you help me solve this problem? So, basically both shared name and name column on this edge table not showing the gene name. It just show like this picture. How can I change the name in the name ...
vania joceline's user avatar
0 votes
1 answer
23 views

Stringapp failed to start in cytoscape

Hello, I encountered a problem of stringapp failed to start. I already reinstall string app 3x but still unable to use string app for creating network of genes. Thank you Vania
vania joceline's user avatar
1 vote
1 answer
20 views

StringApp installed on Cytoscape, But does not added to IMPORT/Network from Public Database

I have different versions of Cytoscape in different PCs. one is 3.10.1 and the other is 3.10.2. for both I installed StringApp but in 3.10.2, It is not added to "import/network from public DB&...
Alireza Ebadi Tabrizi's user avatar
1 vote
0 answers
15 views

How to use cytoscape for nutrigenomics [closed]

I am a doctor, want to use cytoscape for nutrigenomics. Where to start for nutrigenomics. What needs to be the input for analysing different food. Where to get data for analysing different food. What ...
Samprath Nayak's user avatar
2 votes
1 answer
25 views

Overlay pathway over a set of genes in Cytoscape

I'm using for first time Cytoscape. I am working with 10 selected genes with fold-change values in 3 different groups. I am not fishing, I am evaluating gene expression. We are trying to relate these ...
Javier Hernando's user avatar
2 votes
1 answer
22 views

How can I access the Cytoscape infrastructure from a local Python file?

I have bunch of python code that uses cytoscape, specifically the cyrest.cyclient part of cytoscape. I know that the code itself can work, as a colleague of mine has used this previously on a small ...
Mara's user avatar
  • 21
2 votes
1 answer
18 views

Issue with iCTNet2 installation

Has anyone encountered this same installation issue of iCTNet2? I encountered this issue for installation of iCTNet2 via Cytoscape App Manager and similarly via installation from website download/...
rob's user avatar
  • 21
3 votes
1 answer
52 views

Cytoscape for coloring the nodes in the network

I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R? My input is 2 column ...
user avatar
3 votes
1 answer
94 views

How to activate an installed plugin (NetworkAnalyzer) on Cytoscape?

I need to use NetworkAnalyzer to analyse the nodes of a PPI network on Cytoscape, but the pre-installed app is not displayed on the Tools menu. I checked the App Manager, but it shows "Installed&...
Tyto alba's user avatar
  • 143