What is cytoscapeCytoscape is an open source software platform for visualizing molecularinteraction networks and biological pathways and integrating thesenetworks with annotations, gene expression profiles and other statedata. Although Cytoscape was originally designed for biologicalresearch, now it is a general platform for complex network analysisand visualization. Cytoscape core distribution provides a basic setof features for data integration, analysis, and visualization.Additional features are available as Apps (formerly called Plugins).Apps are available for network and molecular profiling analyses,new layouts, additional file format support, scripting, andconnection with databases. They may be developed by anyone usingthe Cytoscape open API based on Java鈩?technology and Appcommunity development is encouraged. Most of the Apps are freelyavailable from Cytoscape App Store. How to install cytoscape
Simple cytoscape usageA toy data (saved in SUPERIOR SUBORDINATEDean Vice dean1Dean Vice dean2Vice dean1 DirectorAVice dean2 DirectorBVice dean1 DirectorCVice dean1 DirectorDDirectorA T1DirectorA T2DirectorB T3DirectorB T4DirectorB T5 The toy network The video tutorial to show how to use More cytoscape operationsNode searching, adding, deletion, selection and attribute chaning
Heatmap nodes color using expression data
Cytoscape mapping gene expression to KEGG pathway
Import a table to construct network
Layout
For example, I have two classes of genes, one is upregulated, the other is downregulated. This information is saved in a two columns file with the first column containing gene names and the second column named Select nodes
Color specific nodes
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