MCODE

Clusters a given network based on topology to find densely connected regions.
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. The newest versions of MCODE (1.5+) also supports *Cytoscape Automation* by providing two commands: * `mcode cluster` * `mcode view`

2.0.0

Works with Cytoscape 3.8

Release Notes

- Renames MCODE's **Node** columns. - Adds the ``MCODE`` namespace to the columns. - The app now creates one set of columns per analysis with the _result number_ (``n``) as suffix: - **MCODE::Score (``n``)** - **MCODE::Node Status (``n``)** - **MCODE::Clusters (``n``)** - MCODE columns are _local_ now (instead of _shared_), which should improve performance in some situations. - The set of MCODE columns are removed when the corresponding result is discarded. - Adds **Apply MCODE Style** option to MCODE's overflow menu. - It now creates 1 style per result (only when this option is selected) and the style is removed when its associated result is discarded. - The correct MCODE style is applied automatically when selecting another result--only if another MCODE style is already set to the same analyzed network view. - It now makes sure that the MCODE panel is open when running the ``cluster`` command. - Fixes automation issue where calling the ``view`` command right after the ``cluster`` one could result in errors because the UI was not ready yet. - Fixes bug that prevents an analysis with the same parameters from being executed again after all results (or the last one) have been removed ("parameters not changed" message). - It now checks all existing results and the error message tells which one has already been executed with the same parameters. - Fixes bug where MCODE columns don't show their values on the _Explore_ panel. - Major performance improvements when creating the cluster images for results with 100+ clusters.

1.6.1

Works with Cytoscape 3.7

Release Notes

- Fixes bug where MCODE *Node* columns (e.g. "MCODE_Score") were not created right away after an analysis, but only after the user selected another MCODE result. - Fixes bug where the cluster *Explore* table were not updated when another MCODE result were selected. - Fixes error that prevented the `mcode cluster` command from returning a successful JSON response.

1.6

Works with Cytoscape 3.7

Release Notes

- Improved user interface that is less cluttered, makes a better use of the available space, and gives the user a couple of new useful features (e.g. Discard All Results). - Fixes bug where a cluster network would not get the correct style. - Fixes bug where MCODE results were not removed after destroying the source network. - Fixes bug that would popup the "parameters not changed" message every time after the first analysis. - Fixes issue where the cluster images would not be displayed in Cytoscape 3.8. - Other minor bug fixes.

1.5.1

Works with Cytoscape 3.6

Release Notes

- Fixes an issue that could prevent a cluster image from being generated when running MCODE for the first time through *commands* or *CyREST*. - Fixes a deadlock that could happen when switching from one *MCODE Result* panel to another.

1.5.0

Works with Cytoscape 3.6

Release Notes

- MCODE now supports *Cytoscape Automation* by providing two commands: - `mcode cluster` - `mcode view` - The Result panel has been improved. - A few minor bug fixes.

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 2.0.0

License Click here

Released 1 Nov 2020

Works with Cytoscape 3.8

Download Stats Click here