Cytoscape 3.10.2 User Manual

The Cytoscape User Manual copyright is owned by The Cytoscape Consortium, and is made available under the same GPL license as Cytoscape itself: LGPL 2.1, the GNU Lesser General Public License, version 2.1, February 1999 available in text at http://www.gnu.org/licenses/lgpl-2.1.html.

Copyright (c) 2001-2024 The Cytoscape Consortium

Table of Contents

• 1. Introduction
• 2. Launching Cytoscape
  • 2.1. System Requirements
  • 2.2. Getting Started
• 3. Command Line Arguments
• 4. Quick Tour of Cytoscape
  • 4.1. Starter Panel
  • 4.2. Basic Features
  • 4.3. The Menus
  • 4.4. Network Management
  • 4.5. Network View Tools
• 5. Creating Networks
  • 5.1. Import Fixed-Format Network Files
  • 5.2. Import Networks from Unformatted Table Files
  • 5.3. Import Networks from Public Databases
  • 5.4. Create a New Network or Edit One Manually
• 6. Nested Networks
  • 6.1. Creating Nested Networks
  • 6.2. Visualization of Nested Networks
• 7. Supported Network File Formats
  • 7.1. SIF Format
  • 7.2. GML Format
  • 7.3. XGMML Format
  • 7.4. SBML (Systems Biology Markup Language) Format
  • 7.5. BioPAX (Biological PAthways eXchange) Format
  • 7.6. GraphML
  • 7.7. Delimited Text Table and Excel Workbook
  • 7.8. Cytoscape.js JSON
  • 7.9. Cytoscape CX
• 8. Node and Edge Column Data
  • 8.1. Import Data Table Files
  • 8.2. Legacy Cytoscape Attributes Format
  • 8.3. Import Data Table from Public Databases
  • 8.4. Mapping Identifiers
• 9. Column Data Functions and Equations
  • 9.1. Column Formulas
  • 9.2. The Formula Builder
  • 9.3. A Note for App Writers
• 10. Finding and Filtering Nodes and Edges
  • 10.1. Search Bar
  • 10.2. The Select Menu
  • 10.3. cyChart
  • 10.4. Filters
  • 10.5. Diffusion
• 11. Navigation and Layout
  • 11.1. Basic Network Navigation
  • 11.2. Other Mouse Behaviors
  • 11.3. Manual Layout
  • 11.4. Node Layout Tools
  • 11.5. Edge Bend and Automatic Edge Bundling
  • 11.6. Automatic Layout Algorithms
  • 11.7. yFiles Layouts
  • 11.8. Layout Parameters
• 12. Styles
  • 12.1. What are Styles?
  • 12.2. Introduction to the Style Interface
  • 12.3. Introduction to Style
  • 12.4. Images, Charts and Gradients
  • 12.5. Styles Tutorials
  • 12.6. Advanced Topics
  • 12.7. Managing Styles
• 13. Network Annotations
  • 13.1. Types of Annotations
  • 13.2. The Annotation Panel
  • 13.3. Creating Annotations
  • 13.4. Selecting Annotations
  • 13.5. Moving Annotations Backwards and Forwards
  • 13.6. Renaming Annotations
  • 13.7. Editing Annotations
  • 13.8. Deleting Annotations
  • 13.9. Grouping Annotations
• 14. Command Panel
• 15. Cytoscape Web Browser
  • 15.1. Cytoscape Web Browser Window
  • 15.2. Cytoscape Web Browser in Results Panel
  • 15.3. Why Cytoscape Web Browser?
• 16. Merge
  • 16.1. Merge Networks
  • 16.2. Merge Tables
• 17. Analyzer
  • 17.1. Network Analysis
  • 17.2. NetworkAnalyzerDemo
• 18. Enrichment Table
  • 18.1. Organism and Gene ID
  • 18.2. Running Enrichment Analysis
  • 18.3. Filter Results
  • 18.4. Charts
  • 18.5. Term Selection
  • 18.6. Optional Settings
  • 18.7. Enrichment Map Generation
  • 18.8. Export results
  • 18.9. Automation
• 19. Cytoscape Preferences
  • 19.1. Managing Properties
  • 19.2. Managing Bookmarks
  • 19.3. Managing Proxy Servers
  • 19.4. Managing Group Settings
  • 19.5. Managing OpenCL Settings
• 20. Linkout
  • 20.1. Adding and Removing Links
• 21. Panels
  • 21.1. Managing Panels
  • 21.2. Other Features
• 22. Rendering Engine
  • 22.1. What is Level of Detail (LOD)?
• 23. Export Your Data
  • 23.1. Raw Data Export
  • 23.2. Exporting for Publication
• 24. Cytoscape and OpenCL (Computing on the GPU)
  • 24.1. What it is for?
  • 24.2. Setup & Configuration
  • 24.3. OpenCL/GPU Troubleshooting
• 25. Cytoscape.js and Cytoscape
  • 25.1. What is Cytoscape.js?
  • 25.2. Data Exchange between Cytoscape and Cytoscape.js
  • 25.3. Export Styles to Cytoscape.js
  • 25.4. Build Your Own Web Application with Cytoscape.js
• 26. Cytoscape Automation
  • 26.1. R and Python Packages
  • 26.2. Commands
  • 26.3. CyREST Interface Layer
• 27. Cytoscape Privacy Policy
• 28. Basic Expression Analysis Tutorial