ClusterMaker

John (Scooter) Morris

University of California, San Francisco

UCSF clusterMaker is a Cytoscape plugin that unifies a number of different clustering techniques and visualizations in a single interface. Current clustering algorithms include Hierarchical and K-Means for clustering expression or genetic data, and MCL and FORCE for clustering similarity networks to look for protein families (and putative functional similarities). Hierarcical clusters may be visualized as hierarchical groups or using the familiar TreeView heat map. K-Means clusters may also be visualized either as groups or as heat maps. In either case, edge attributes may be used to view a symmetrical heatmap. MCL and FORCE both create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network. The clusterExplorer plugin may also be used after clustering with MCL and FORCE to explore cluster statistics and relationships. clusterMaker depends on version 2.6.1 of Cytoscape and will be available from the Cytoscape plugin manager or at http://www.rbvi.ucsf.edu/research/cytoscape/clusterMaker after 2.6.1 releases.

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