Cytoscape App Store - clusterMaker2

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Release History

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: * AutoSOME * Create correlation network * Hierarchical * K-Means * K-Medoid * HOPACH * PAM The current network partitioning algorithms are: * Affinity propagation * AutoSOME * Fast Greedy (run remotely) * Cluster "Fuzzifier" * Connected Components * Community Clustering (GLay) * Fuzzy C-Means Clustering * Infomap (run remotely) * Leiden (run remotely) * Label propagation (run remotely) * Leading Eigenvector (run remotely) * MCL * MCODE * Multilevel cluster (run remotely) * 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 9 dimensionality reduction techniques: * Isomap (run remotely) * Local Linear Embedding (run remotely) * MDS (Multi-Dimensional Scaling - run remotely) * PCA * PCoA * Spectral (run remotely) * t-SNE * t-SNE (run remotely) * UMAP (run remotely) 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)

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2.3.4

Works with Cytoscape 3.9

Release Notes

More bug fixes: 1. Several updates to support better handling of backend (server) errors. These errors are now propagated to user interface, usually in the user log. 1. Fix to the remote tSNE to change argument from "PCA" to "pca", as documented in igraph.

2.3.3

Works with Cytoscape 3.9

Release Notes

Two simple bug fixes: 1. Improve handling of results with a large number of clusters. 1. Avoid a thread deadlock

2.3.2

Works with Cytoscape 3.9

Release Notes

Three bug fixes in this release: 1. Handle non-Double columns when evaluating attributes 1. Make sure we always use the correct JobHandler. This broke several remote algorithms. 1. When creating a new network view after a remote execution, don't create the context, which would bring up a Tunable panel that wound up in a deadlock. We already have that information.

2.3.1

Works with Cytoscape 3.9

Release Notes

Several update: * Fix missing handling of some arguments * Add export function to scatter plots * Add improved control over the loadings vectors in the PCS plot * Fixes for AutoSome algorithm

2.2

Works with Cytoscape 3.9

Release Notes

A couple of major fixes, and some minor ones: * Fixed broken argument passing -- arguments from GUI are now successfully passed to remote server for execution. * Fixed exporting from scatter plot to correctly match pan and zoom in plot. Also increased bitmap export to much higher density. * Fixed minor user interface issue in scatter plot where changes would result in a complete repaint (and rescale) of the entire plot. * Fixed sense of "Synchronous" for remote executions. Previously, synchronous=true actually meant run asynchronously.

2.0

Works with Cytoscape 3.8

Release Notes

This represents a major update to clusterMaker, with the addition of several new algorithms and support of remote execution. The remote execution utilizes the Cytoscape "jobs" framework and will allow many of the algorithms to run on servers provided by the RBVI. The jobs are executed asynchronously and the results are loaded by clicking on the green cloud icon in the lower left-hand corner of the Cytoscape window.

1.3.1

Works with Cytoscape 3.6

Release Notes

Fixed a bug in Hierarchical Clustering that prevented symmetric edge clusters from working.

1.2.1

Works with Cytoscape 3.3

Apps that depend on this release

Release Notes

Mostly some bug fixes: 1. Provided two different approaches to handling residuals in MCL. 2. Fixes a bug in K-means derived abstract clusterers that skipped updating the attribute clustering.

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.