Data Science Training Program
Tuesday, November 9, 2021

Alex Pico

Core Director

In this course, you’ll learn about the integration of Cytoscape 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 how to access and control Cytoscape from R/Python 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 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. See introductory and intermediate courses:

Visit the workshop site for more details and materials.

View the complementary workshops at UCSF.


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

The Gladstone Data Science Training Program was started in 2018 to provide trainees with learning opportunities and hands-on workshops to improve their skills in bioinformatics and computational analysis. This program offers a series of workshops throughout the year to enable trainees to gain new skills and get support with their questions and data.

Diversity, Equity, and Inclusion

At Gladstone, we are committed to providing events and professional development activities that resonate with our community’s diverse members. Our goal is to develop creative programming that encompasses a wide variety of ideas and perspectives to inspire, educate, and engage with everyone within our walls.

We want to effect positive change through our events and activities by providing a platform for discussions on important topics related to increasing diversity and inclusiveness in the sciences.