Portal:Cytoscape

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Welcome to Cytoscape 2.x at Open Tutorials

The purpose of this portal is to distribute tutorial materials for Cytoscape 2.x and Cytoscape 2.x plugins.

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.

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Available Tutorials

Basic

Image:bullet.png Introduction to Cytoscape, part 1

Image:bullet.png Introduction to Cytoscape, part 2

Image:bullet.png Filtering and Editing

Image:bullet.png Basic Expression Analysis - Yeast

Image:bullet.png Basic Expression Analysis - Human

Image:bullet.png Network Loading and ID Mapping

Advanced

Image:bullet.png Cytoscape Developers Tutorial

Plugins

Image:bullet.png Assorted Cytoscape Plugins

Image:bullet.png Agilent Literature Search

Image:bullet.png MiMiPpi Discovery

Image:bullet.png Structure Visualization and Structure Function Linkage Database

Image:bullet.png Google Charts Plugin - Creating Pie Charts on Nodes

Analysis plugins

Image:bullet.png Cluster Maker

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 1

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 2

Image:bullet.png Cluster Maker BMC Bioinformatics Scenario 3

Image:bullet.png DomainGraph

Image:bullet.png MCODE Plugin Demo

Image:bullet.png Network Analyzer

Layout plugins

Image:bullet.png Community Structure Layout

Image:bullet.png Cytoscape Cerebral Plugin

Image:bullet.png Power Graph Analysis with CyOog


3.0 tutorials

Image:bullet.png Cytoscape 3.0 Tutorials

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Other Resources

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