Cytoscape 3.9

• Major new features:
  • Table styles -- can set up mappings for table columns
  • Improved performance for large networks
  • Support for edge Z order
  • Haystack edges
  • Copy/paste for annotations
  • Annotation and label rotation
  • New equations editor
  • Commands to create and modify annotations
• Release date?
  • Hopefully sometime in Q2
• Nightly builds available at:
  https://cytoscape-builds.ucsd.edu/cytoscape-builds/Cytoscape-3.9.0/nightly/

Cytoscape 3.9 Demo

Cytoscape Automation

Cytoscape Automation

• RCy3
  • 100's of methods to simply interaction between R scrips and Cytoscape, including:
    • Create networks from igraph or graphNEL objects
    • Load networks from Cytoscape into R
    • Create and change styles
    • Load tables from R data frames
    • Load R data frames from Cytoscape
  • Available via bioconductor
• py4cytoscape
  • Generally, provides equivalent functionality as RCy3
  • Available via pypy