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Questions tagged [cytoscape]

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Various apps are available for different problem domains, including bioinformatics, social network analysis, and semantic web.

Cytoscape (not to be confused with the JavaScript library ) is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization.

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Arrange Cytoscape network windows using the API (Version 3)

I'm developing a bundle app for Cytoscape 3. In this app I need a funcionality very similar to the build-in View > Arrange Network Windows > Grid, or Ctrl+G. However, I cannot seem to find anything in Cytoscape's API that allows me to arrange…
T.S.
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Importing Cytoscape Desktop 3.1 BETA exported JSON file (.cyjs) to Cytoscape.js

I exported a protein-protien network from Cytoscape 3.1 BETA 3 using the built-in exporter to a JSON (cyjs) file. I tried to import this cyjs file to a web application using Cytoscape.js library but I failed. I read the question asked by gcpdev…
Zoliqa
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Using jung2 in cytoscape plugins

I've taken up java for about a week and a half now with an eye toward writing cytoscape plugins and using jung2 to analyze and manipulate cytoscape graph objects. Is there any way to extend the cytoscape graph object call it class xyz to include a…
Stephen Kauffman
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i need code for hyperlink that is activated while clicking on nodes?

I have to view my data as a visual network format so used cytoscape web. I have used example link http://lekshmideepu.blogspot.in/2012/03/cytoscape-web-examples.html for my drawing a network with different colored nodes and edges,It works color and…
user2502386
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How to draw pie chart in Cytoscape(or any JavaScript) tree

I have use Cytoscape javascript to draw a Tree. The problem is I want to display many of value in a node, so we decide to draw the pie chart instead of it's original circle to represent many value. But I don't know how to draw pie chart over a…
JiratPasuksmit
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Cytoscape 3.0 Bundle App

I'm trying to create a new Cytoscape 3.x application following the Create a Bundle App Using IDE tutorial with no luck. The tutorial is quite easy to follow, however when I run Cytoscape to find out if my app is running, I can see that it is listed…
Jose Villaveces
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R and cytoscape importing networks

I tried using the RCytoscape package to export networks from R to cytoscape. I tried to follow the documentation butfailed. The following are the commands Iused: data(liver.toxicity) X <- liver.toxicity$gene Y <-…
Stacey John
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is background list of genes in CluoGO in Cytoscape are modify for gene enrichment analysis?

I want to modify background list gene in the CluoGO. anybody know hot i can change the list of this genes for gene enrichment analysis? and use the restricted list for background. thanks There are not any options for the modify of gene list…
sat van
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Why do I keep getting an error for index length when I try to build a Cytoscape enrichment map from GSEA data?

I am new to Cytoscape and GSEA, but am trying to build an enrichment map with my RNA-seq data. I have uploaded the .gmt file and two .xls files, one for positive enrichment and one for negative. I also have a .rnk file but that doesn't seem to be…
KBO
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Create tooltips on Cytoscape Nodes Label using popper and tippy

I am trying to use cytoscape with tippy but it is not showing any tool tips. It throws an error that ele.popperRef is not a function. Here is the stackblitz link: https://stackblitz.com/edit/dagre-tippy?file=src%2Fapp%2Fapp.component.ts I have added…
Learn AspNet
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How would generate a Markov matrix from the graph below?

I am using CytoScape software. It has the ability to create a MCL Cluster automatically but I am having difficulties seeing the Associated Matrix. Does anyone know how to get that using Cytospace? mcl cluster generated using clustermaker2
dp758
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Astray cytoscape indentifying floating values as integer

When I import node data from .xlsx file, I found some floating variables would be considered as integer ones, which finally leads to an uncorrect input (for example, 0.3-->0). After some search on-line, I found some information about it in official…
Weber Huang
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How do I install Cytoscape on Google Colab?

I'd like to use Cytoscape.js (https://js.cytoscape.org/) on Google Colab. I found here (https://py2cytoscape.readthedocs.io/en/latest/) that this can be done in Jupyter Notebooks, but the documentation isn't very thorough. Here is the code I ran to…
rchurt
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Cytoscape won't let me upload table to a network collection the only option was to unassigned table. Does anyone know how to resolve this?

the drop-down option isn't available so my table is automatically imported as unassigned table. Anybody come across this issue before? Or is there something wrong with my table setting? cytoscape screenshot
user13581130
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Analyze networks which are not scale free

I am trying to analyze the graph constructed with networkx having around 7000 nodes. When I plot the degree distribution there are nodes that are far away from the fitted power law as shown in the attached plot. This means the network is not…
hemanta
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