Intermediate Cytoscape Networks and Omics Data Visualization

Description

This course is a complement to “Introduction to Network Biology and Cytoscape” from the previous day. Following a brief review of the key concepts of network analysis, we will embark on a deep dive into data visualization and advanced Cytoscape features. We will work through three prepared use cases demonstrating various omics data types and strategies. You are encouraged to bring your own data as well. By the end of this course you will be able to:

• Know when and how to use Cytoscape in your research
• Handle multiple data types in Cytoscape
• Transform and merge data with networks from multiple sources
• Master customized data visualization
• Navigate the greater Cytoscape ecosystem.

Prerequisites: You should already be familiar with Cytoscape and the fundamentals of network analysis (see prior course). Bring a laptop with the latest version of Cytoscape installed.

Learning Path

   This is an intermediate workshop in the Network Analysis and Visualization series. You should already be familiar with Cytoscape prior to attending this workshop. See introductory course:

• Introduction to Cytoscape and Network Biology

Materials

• Online slides

Pre-workshop Instructions

Please go through this pre-workshop checklist before the class:

1. Install the latest version of Cytoscape:
   • Download from: https://cytoscape.org/download.html
   • Launch installer and complete installation
2. (Optional) If you are facing a network visualization challenge with your current data, bring it to the workshop!

Online Learning

You can access these materials remotely at any time and go through them at your own pace. Here's how:

1. Perform the pre-workshop instruction steps above.
2. Access the Online Slides above.
3. 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.
4. Example datasets are provided toward the end of the presentation.
5. Contact [email protected] with any questions you have and we will reply promptly. For Cytoscape-specific questions, you can access a larger community of help here.