Cytoscape 2.3 User Manual


Table of Contents

Cytoscape 2.3.1 User Manual
Introduction
Launching Cytoscape
Quick Tour of Cytoscape
The Menus
Network Management
The Network Overview Window
Command Line Arguments and Properties
Command Line Arguments
Cytoscape Properties
Building and Storing Interaction Networks
Loading Gene Expression (Attribute Matrix) Data
Node and Edge Attributes
Navigation and Layout
Navigation
Automatic Layout Algorithms
Manual Layout
Visual Styles
Introduction to Visual Styles
Visual Attributes, Graph Attributes and Visual Mappers
Visual Styles Tutorials
Managing Visual Styles
Editing Networks
CytoPanels
Rendering Engine
Annotation
Gene Ontology Server Wizard
Filters
LinkOut
Acknowledgements
Appendix A: Old Annotation Server Format
Gene Ontology Server Wizard
Building your own annotation files
Load Data into Cytoscape
Getting and Reformatting GO Data
Appendix B: GNU Lesser General Public License

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Cytoscape 2.3.1 User Manual

This document is licensed under the Creative Commons license, 2006

Authors: The Cytoscape Collaboration

The Cytoscape project is an ongoing collaboration between:

Table 1. 

University of California at San Diego

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Institute for Systems Biology

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Memorial Sloan-Kettering Cancer Center

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Institut Pasteur

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Agilent Technologies

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Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.