Coral: an integrated suite of visualizations for comparing clusterings

Download CORAL with sample data:

• runnable jar
  To run:
  ./coral
  to run shell script or
  java -Xmx1G -jar coral.jar
  to run the jar
• Mac OS app
  Unzip and run
  coral.app

Check it out on GitHub!

Filippova D, Gadani A, Kingsford C. Coral: an integrated suite of visualizations for comparing clusterings. To Appear. BMC Bioinformatics, 2012. pdf
Filippova, D, Gadani, A, Kingsford, C. Coral: an integrated suite of visualizations for comparing clusterings of biological data. ISMB 2012. pdf

Network clustering:

• CFinder (requires registration)
• Graph Summarization (requires registration)
• Link clustering
• MCODE (Cytoscape)
• MINE (Cytoscape)
• MCL
• NeMo (Cytoscape)
• SPICi

Sequence clustering:

• DNACLUST
• Scimm
• CompostBin
• GraphClust (RNA structure)

Gene expression data clustering:

• Dynamic Tree Cut (R package)