Advanced Cytoscape Automation
In this course, we will demonstrate 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, we will 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 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 and 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: