clusterMaker2

Multi-algorithm clustering app for Cytoscape
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)

1.1.0

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

clusterMaker2 1.1 improves performance and adds new algorithms as well as entirely new classes of analyses that allow users to rank clusters using orthogonal data and perform dimensionality reduction techniques, including PCA, PCoA, and t-SNE. We've also significantly improved the performance of some of the existing algorithms, most notably MCL.

0.9.5

Works with Cytoscape 3.2

Apps that depend on this release

Release Notes

Synchronized with the latest release of MCODE. Also added support for multiple results panels of different clusterings.

0.9.4

Works with Cytoscape 3.2

Release Notes

This version of clusterMaker has several bug fixes, but more importantly it adds a new ResultsPanel visualization that shows the individual clusters for network partitioning algorithms. There are also some new algorithms, including the Cheng&Church bicluster algorithm.

0.9.3

Works with Cytoscape 3.1


0.9.2

Works with Cytoscape 3.1

Release Notes

Updated with fixes for the case where edges don't have any weights.

0.9.1

Works with Cytoscape 3.1


0.9.0

Works with Cytoscape 3.1


CYTOSCAPE 3

Version 1.1.0

Released 27 Apr 2017

Works with Cytoscape 3.3

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