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Current Apps (3.x)

News

October 22, 2018

Cytoscape v3.7 has been released. See the release notes for what's new.

March 27, 2017

Cytoscape v3.5 has been released. Releases at the 2.x level are no longer supported.

August 25, 2011

Cytoscape 2.8.2 has been released! This release provides a number of bug fixes, usability improvements, and a significantly improved memory detection and allocation process. Check it out at http://www.cytoscape.org.

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UCSF RBVI Cytoscape Apps

The Resource for Biocomputing, Visualization, and Informatics (RBVI) focuses on creating innovative computational and visualization-based data analysis methods and algorithms, implementing them as professional-quality, easy-to-use software tools, and applying these tools to solve a wide range of biomedical research problems. Our historical emphasis has been on developing tools for structural biology, such as the broadly used molecular modeling package, UCSF Chimera.

Recognizing the importance of biological context in understanding the sequence→structure→function triad, we are also developing tools for the analysis and visualization of networks with Cytoscape, a widely used open-source tool. Cytoscape provides an excellent “app” mechanism that we have used to add functionality, and we also participate in the development of the Cytoscape core.

Highlighted App

clusterMaker

Clustering and Visualizing Expression Data

In this screenshot the expression data in the sampleData file galFiltered.cys has been clustered using the hierarchical clusterer and visualized using a heatmap with associated dendogram. The groups created by the cluster are shown on the network.

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