Alex Pico, PhD
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. The 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
Prerequisites: You should already be familiar with Cytoscape and the fundamentals of network analysis (see prior courses). You should already have experience with R (or Python) and scripting bioinformatics analyses. Bring a laptop with the latest version of Cytoscape installed. Instructions will be provided prior to the course for installing RStudio, specific R packages, and Cytoscape apps.
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:
- Introduction to Cytoscape and Network Biology for Biologists
- Introduction to Cytoscape and Network Biology for CS
- Intermediate Cytoscape for Omics Data Visualization
- Introduction to R for data analysis
- Intermediate R for data visualization
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.