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Advanced Cytoscape Using R

November 9, 2021 @ 1:00 pm - 4:00 pm

In this course, you’ll learn about the integration of Cytoscape into programmatic workflows and pipelines using R. Following a brief review of the goals and capabilities of Cytoscape in network analysis, you’ll learn how to translate these into scriptable use cases for practical applications.

The bulk of the course will be a hands-on demonstration of how to access and control Cytoscape from R to perform a network analysis of tumor expression and variant data. These principles can be extended to other data types and research questions, as well as to Python and other automation environments.

By the end of this course you will be able to:

  • Command programmatic control over Cytoscape,
  • Perform network construction, data loading, analysis, and visualization
  • Integrate Cytoscape into your bioinformatics pipelines
  • Compose your own complex network analysis workflows
  • Pull together various tools and resources into a single script



  • Familiarity with Cytoscape and the fundamentals of network analysis
  • Experience with R (or Python) and scripting bioinformatics analyses
  • Laptop with the latest version of Cytoscape installed

You’ll receive instructions prior to the course for installing RStudio and specific R packages and Cytoscape apps.

Advanced: This is an advanced workshop in the Network Analysis and Visualization series. You should already be familiar with both Cytoscape and R prior to attending this workshop.


Visit the workshop site for more details and materials.

Register here