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= Cytoscape @version@ User Manual = <<TableOfContents(3)>>
<<Include(/TitlePage,"Cytoscape @version@ User Manual")>>
<<Include(/LaunchingCytoscape,"Launching Cytoscape")>>
<<Include(/Quick_Tour,"Quick Tour of Cytoscape")>>
<<Include(/Command_Line_Arguments,"Command Line Arguments")>>
<<Include(/Preferences,"Cytoscape Preferences")>>
<<Include(/Creating_Networks,"Creating Networks")>>
<<Include(/Network_Formats,"Supported Network File Formats")>>
<<Include(/Attributes,"Node and Edge Attributes")>>
<<Include(/Attribute_Formulas,"Attribute Functions and Equations")>>
<<Include(/Expression_Data,"Loading Gene Expression (Attribute Matrix) Data")>>
<<Include(/ImportingNetworksFromWebServices, "Importing Networks and Attributes from External Databases")>>
<<Include(/Navigation_Layout,"Navigation and Layout")>>
<<Include(/Visual_Styles,"Visual Styles")>>
<<Include(/Filters,"Finding and Filtering Nodes and Edges")>>
<<Include(/Network_Editor,"Editing Networks")>>
<<Include(/Nested_Networks, "Nested Networks")>>
<<Include(/Plugins,"Plugins and the Plugin Manager")>>
<<Include(/Rendering_Engine,"Rendering Engine")>>
<<Include(/LGPL_License,"Appendix A: GNU Lesser General Public License")>>
<<Include(/How_to_increase_memory_for_Cytoscape,"Appendix B: Increasing memory for Cytoscape")>>


  1. Cytoscape @version@ User Manual
  2. Introduction
  3. Quick Tour of Cytoscape
    1. Welcome Screen
    2. Basic Features
      1. Network Editing
    3. The Menus
      1. File
      2. Edit
      3. View
      4. Select
      5. Layout
      6. Apps
      7. Tools
      8. Help
    4. Network Management
      1. Arrange Network Windows
    5. The Network Overview Window
  4. Command Line Arguments
  5. Cytoscape Preferences
    1. Managing Properties
    2. Managing Bookmarks
    3. Managing Proxy Servers
    4. Managing Group View
  6. Creating Networks
    1. Import Fixed-Format Network Files
      1. Load Networks from Local Computer
      2. Load Networks from a Remote Computer (URL import)
    2. Import Networks from Unformatted Table Files
      1. Supported Files
      2. Basic Operations
      3. Advanced Options
      4. Modify Column Name/Type
    3. Import Networks from Public Databases
      1. Getting Started
      2. Example: Retrieving Protein-Protein Interaction Networks from Multiple Databases
    4. Create a New Network Manually
      1. Adding a Node
      2. Adding an Edge
      3. Grouping nodes
      4. Adding Network Annotations
  7. Supported Network File Formats
    1. SIF Format
      1. Delimiters
    2. NNF
      1. Examples
    3. GML Format
    4. XGMML Format
    5. SBML (Systems Biology Markup Language) Format
    6. BioPAX (Biological PAthways eXchange) Format
    7. PSI-MI Format
    8. GraphML
    9. Delimited Text Table and Excel Workbook
    10. Cytoscape.js JSON
  8. Node and Edge Attributes
    1. Table data
      1. Importing data
      2. Table Panel
    2. Ontologies
      1. Ontology and Association File Format
      2. Import Gene Ontology and Gene Association Files
  9. Navigation and Layout
    1. Basic Network Navigation
      1. Other Mouse Behaviors
    2. Automatic Layout Algorithms
      1. yFiles Layouts
      2. Layout Parameters
    3. Edge Bend and Automatic Edge Bundling
    4. Manual Layout
      1. Node Movement and Placement
  10. Finding and Filtering Nodes and Edges
    1. Search Bar
    2. Filters
      1. Narrowing Filters
      2. Chainable Filters
      3. Working with Narrowing and Chainable Filters
    3. The Select Menu
  11. Editing Networks
    1. Adding Node
    2. Adding Edge
  12. Nested Networks
    1. Creating Nested Networks
    2. Visualization of Nested Networks
  13. Rendering Engine
    1. What is Level of Detail (LOD)?
      1. Parameters for Controlling LOD
      2. Force to Display Detail
  14. Annotation
    1. Ontology and Annotation File Format
    2. Default List of Ontologies
    3. Gene Association File
    4. Import Ontology and Annotation
  15. Linkout
    1. Adding and Removing Links

Cytoscape @version@ User Manual

This is a legacy document

This page has been deprecated and is no longer updated. The current version of the Cytoscape manual can be found at http://manual.cytoscape.org/

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) 2001-2015 The Cytoscape Consortium


This is a legacy document

This page has been deprecated and is no longer updated. The current version of the Cytoscape manual can be found at http://manual.cytoscape.org/

Cytoscape @version@ is the latest version of Cytoscape, building upon the new architecture, developer API and set of user controls established in the 3.x series. If you're familiar with former versions of Cytoscape, this version will feel completely familiar and you'll be all set to go. In future releases, we will continue to tweak and improve both the software and the documentation. This manual will be updated to reflect all the latest changes.

This manual describes the installation and use of Cytoscape. For a more thorough understanding of Cytoscape and its ecosystem, we highly recommend reading the Welcome Letter accessible on the http://cytoscape.org website.

Cytoscape_3/UserManual (last edited 2016-04-26 20:01:35 by server2)

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

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