Advanced Cytoscape Automation

In this course, you’ll learn how Cytoscape can be integrated into programmatic workflows and pipelines using R or Python.

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 accessing and controlling Cytoscape from R/Python to perform a network analysis of tumor expression and variant data. The principles can be extended to other data types and research questions, as well as to other automation environments. 

By the end of this course you’ll 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

Bring a laptop with the latest version of Cytoscape installed.

Visit the workshop site for more details and materials.

Advanced Level: This is an advanced workshop in the Network Analysis and Visualization series. Prior to attending this workshop, you should already be familiar with Cytoscape and the fundamentals of network analysis, as well as have experience with R or Python and scripting bioinformatics analyses.

See introductory and intermediate courses:

• Introduction to Cytoscape and Network Biology
• Intermediate Cytoscape for Omics Data Visualization
• Introduction to R for data analysis
• Intermediate R for data visualization