UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back
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clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.
BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.