Cytoscape and Single Cell Analysis

Slides: http://tutorials.cytoscape.org

John "Scooter" Morris

EBI Single Cell Workshop
April 26-30 2021

Hands-on Exercise

scNetViz - Single-cell RNASeq analysis

Feedback & Future Directions

• What was most useful about scNetViz?
• What was most difficult about using scNetViz?
• Suggestions for enhancements?
• Things we would like to do next:
  • More server-side processing
    • Cache large data sets on the server
    • Perform DE processing server-side
    • Do we need TPM and Categories tables?
  • Support for HCA dcp4 files
    • Matrices in dcp4 are loom format only
    • We'll need to handle them server-side (no Java bindings for loom)
  • Column mapping (ensemble->gene names)

Q&A