MCODE

Clusters a given network based on topology to find densely connected regions.
Categories: clustering, graph analysis
MCODE finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families.

1.4.2

Works with Cytoscape 3.3

Release Notes

- Fixes issue which could make Cytoscape run out of memory and freeze when running the analysis on large networks. - MCODE algorithm is now parallelized, which should improve the speed of analysis of large networks on computers with multiple cores. - Fixes error when performing the analysis on a network without a view in Cytoscape 3.4. - Minor UI improvements.

1.4.1

Works with Cytoscape 3.2

Release Notes

- Fixes bug that changed the k-core calculation when multiple edges were present--MCODE now only counts "merged" edges in order to get the degree of a node. - The cluster network (and cluster image) does not contain loops anymore if that option is false. - Fixes AWT thread deadlock that happened when MCODE showed the "No clusters were found" message dialog. - It no longer clears the clusters selection when switching between MCODE results. - MCODE panels are now disposed after the app is uninstalled or another version is installed. - UI improvements.

1.4.0

Works with Cytoscape 3.0

Release Notes

- Fixes bugs that affected the calculation of network density.

1.4.0.beta2

Works with Cytoscape 3.0


1.4.0.beta1

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.4.2

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Released 9 Jun 2016

Works with Cytoscape 3.3

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CYTOSCAPE 2

Version 1.32

Released 28 Jun 2011

Works with Cytoscape 2.6, 2.7, 2.8

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