Introduction to Cytoscape:

Slides: https://cytoscape.org/cytoscape-tutorials/presentations/intro-cytoscape-2021-ismb.html#/


John "Scooter" Morris

ISMB/ECCB 2021 Tutorial: Reproducible omics data analysis workflows
July 22-23 2021

Goals and Motivations

By the end of these sessions you should be able to:

  • Understand the major applications of network biology
  • Find relevant networks and pathways
  • Import your data into Cytoscape
  • Perform basic topological and other network analyses
  • Perform network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials
  • Get started on using Cytoscape from R or Python
Introduction To Network Biology Finding Network Data Network Analysis and Viz Introduction to Cytoscape Hands-on Exercises Q&A

Introductions

John "Scooter" Morris, UCSF
  • Executive director, Resource for Biocomputing, Visualization, and Informatics
  • Roving Engineer, National Resource for Network Biology
  • Cytoscape team since 2006
  • Author of over two dozen Cytoscape apps

Caveats

  • There are many more slides than we have time for
  • Depending on your interests, we will skip entire sections
  • The slides will continue to be available for your reference
Introduction To Network Biology Finding Network Data Network Analysis and Viz Introduction to Cytoscape Hands-on Exercises Q&A
Introduction To Network Biology Finding Network Data Network Analysis and Vis Introduction to Cytoscape Hands-on Exercises Q&A
Introduction To Network Biology Finding Network Data Network Analysis and Vis Introduction to Cytoscape Hands-on Exercises Q&A

Tour of Cytoscape


  1. Launch the latest version of Cytoscape

Tour of Cytoscape


  1. Open CyBrowser
  2. Enter URL: tutorials.cytoscape.org

Tour of Cytoscape


  1. Click on Tour of Cytoscape
  2. Resize window to your preference

Tour of Cytoscape

Follow-along walkthrough:

  1. Loading networks
  2. Loading tables
  3. Selection and filtering
  4. Changing visual attributes
  5. Exporting images
  6. Saving sessions
Introduction To Network Biology Finding Network Data Network Analysis and Vis Introduction to Cytoscape Hands-on Exercises Q&A

Hands-on Exercises

  1. Bulk RNA-Seq workflow: RNA-Seq Data Network Analysis
  2. Biological scenario: Basic Data Visualization

Hands-on Exercises


What have we learned?
Introduction To Network Biology Finding Network Data Network Analysis and Vis Introduction to Cytoscape Hands-on Exercises Q&A

Q&A

Thank You!

Here are additional resources you may find useful:

Thank You!




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