SCPS (Spectral Clustering of Protein Sequences).Gene expression analysis in a network context.įinding complexes in proteomic and genetic interaction data.įunctional annotation by clustering protein similarity networks. In the BMC Bioinformatics publication: " clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape", currently submitted. The other three tutorials describe the steps necessary to reproduce the scenarios described The first tutorial:Ĭluster Maker covers some of the basic featuresĪnd uses of clusterMaker. Open Tutorials web site under the "Cytoscape Tutorials" section. In addition to this documentation, there are four tutorials available on the "meta nodes" to allow interactive exploration of the putative familyĪssociations within the Cytoscape network, and results may alsoīe shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back.ĬlusterMaker requires version 2.8.2 or newer of CytoscapeĪnd is available from the Cytoscape plugin manager under Hierarchical, k-medoid, AutoSOME, and k-means clusters may beĭisplayed as hierarchical groups of nodes or as heat maps.Īll of the network partitioning cluster algorithms create collapsible MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity K-means for clustering expression or genetic data and MCL, transitivity clustering, affinity propagation, Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and UCSF clusterMaker is a Cytoscape plugin that unifiesĭifferent clustering techniques and displays into a single In this screenshot, theĮxpression data in the sampleData file galFiltered.cys has been clustered using the hierarchical methodĪnd displayed as a heatmap with associated dendrogram.
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