Categories: automation, clustering, data visualization, gene expression, grouping, heat map visualization, visualization

clusterMaker2 is the Cytoscape 3 version of the clusterMaker plugin. clusterMaker2 provides several clustering algorithms for clustering data within columns as well as clustering nodes within a network. This version also provides support for two new algorithms: Fuzzy C-Means and a new "Fuzzifier". In addition to providing clustering algorithms, clusterMaker2 provides heatmap visualization of both node data and edge data as well as the ability to create new networks based on the results of a clustering algorithm. Current node attribute algorithms: * Hierarchical * K-Means * K-Medoid * AutoSOME * Create correlation network * PAM * HOPACH * DBSCAN The current network partitioning algorithms are: * Affinity propagation * Cluster "Fuzzifier" * Connected Components * Community Clustering (GLay) * Fuzzy C-Means Clustering * MCODE * MCL * SCPS (Spectral Clustering of Protein Sequences) * Transitivity Clustering four post-cluster filters: * Best Neighbor filter * Cutting Edge filter * Density filter * Haircut filter five cluster ranking algorithms: * Additive sum * Multiply sum * Page Rank * Page Rank with priors * Hyperlink induced topic search and 3 dimensionality reduction techniques: * PCA * PCoA * t-SNE In addition, clusterMaker2 provides 5 ways to visualize the data: * Create New Network from Attribute * Create new Network from clusters * JTree TreeView * JTree KnnView * JTree HeatMap view (unclustered)

Authors:

• John "Scooter" Morris (UCSF)
• Leonard Apeltsin (UCSF)
• Aaron Newman (Stanford University)
• Jan Baumbach (University of Southern Denmark)
• Tobias Wittkop (Buck Institute)
• Gang Su (University of Michigan)
• Gary Bader (University of Toronto)
• Abhiraj Tomar (University of Southern California)