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:
- 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
You can access these materials remotely at any time and go through them at your own pace. Here's how:
- Perform the pre-workshop instruction steps
- Access the online slides.
- Go through the slides at your own pace. Speaker notes are available for non-obvious slides. Press 's' to pop-up the speaker view. Navigate the slides by 'spacebar' or 'down arrow' to go through each module.
- Three hands-on exercises are recommended at the end of the presentation, starting here.
- Contact bioinformatics@gladstone.ucsf.edu with any questions you have and we will reply promptly. For Cytoscape-specific questions, you can access a larger community of help here.