Table of Contents
- Cytoscape User Manual
- Introduction
- Launching Cytoscape
- Quick Tour of Cytoscape
- Command Line Arguments
- Cytoscape Preferences
- Creating Networks
- Supported Network File Formats
- Node and Edge Attributes
- Attribute Functions and Equations
- Loading Gene Expression (Attribute Matrix) Data
- Importing Networks and Attributes from External Databases
- Web Service Client Manager
- Getting Started
- Example #1: Retrieving Protein-Protein Interaction Networks from IntAct
- Example #2: Retrieving Protein-Protein Interaction Networks from NCBI Entrez Gene
- Example #3: Retrieving Pathways and Networks from Pathway Commons
- Future Directions
- Import Attributes from External Database
- Use Multiple Services in a Workflow
- Navigation and Layout
- Visual Styles
- Finding and Filtering Nodes and Edges
- Editing Networks
- Nested Networks
- Plugins and the Plugin Manager
- CytoPanels
- Rendering Engine
- Annotation
- Linkout
- Acknowledgements
- Appendix A: Old Annotation Server Format
- Appendix B: GNU Lesser General Public License
- Appendix C: Increasing memory for Cytoscape
This document is licensed under the Creative Commons license, 2006
Authors: The Cytoscape Collaboration
The Cytoscape project is an ongoing collaboration between:
University of California at San Diego | |
Institute for Systems Biology | |
Memorial Sloan-Kettering Cancer Center | |
Institut Pasteur | |
Agilent Technologies | |
University of California at San Francisco | |
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.