#Cluster treeview download#

To download clusterMaker using the plugin manager, Create New Network with Nested Networks from AttributeĬlusterMaker is available through the Cytoscape plugin manager orīy downloading the source directly from the Cytoscape svn repositoryĬytoscape Subversion Server information, or browse the csplugins/ucsf/scooter/clusterMaker.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. To compile or test the external files, you can right click on the folder and select 'Compile Folder' or 'Test Folder'.Figure 1. 'Test All' will only tess open project source and auxiliary files. The 'Compile All' button only compiles open project source and auxiliary files, instead of all open files.

The behavior of some of the buttons also changes in Tree View. To move a file from the External Files branch to the Included External Files branch, right click on the file in the tree listing, and select the appropriate option at the bottom of the menu. They are compiled and tested with the project and are opened whenever the project is opened. Included External Files: Files that are located outside of the project directory but that are still important to the project. They will never be compiled or tested as part of your project. It is important to put the project file in the root of your project hierarchy.Įxternal Files: Files that are not in the project directory. Thus, the location of your project file determines what files are part of your project. Source Files: All files located in or below the project file's directory(project directory).