CyCommunityDetection

Integrates multiscale community detection and functional enrichment for network analysis. CDAPS
Categories: CDAPS, clustering, Community detection, Gene Ontology, network analysis
CyCommunityDetection, the Cytoscape App component of Community Detection APplication and Service (CDAPS), performs multiscale community detection and functional enrichment for network analysis through a service-oriented architecture. These features are provided by integrating popular community detection algorithms and enrichment tools. All the algorithms and tools run remotely on a dedicated server. Currently supported features: * Community detection algorithms: [Louvain](https://github.com/idekerlab/cdlouvain), [Infomap](https://github.com/idekerlab/cdinfomap), [OSLOM](http://www.oslom.org), [CliXO](https://github.com/idekerlab/cdclixo), [HiDeF](https://github.com/idekerlab/cdhidef) * Functional enrichment tools: [g:Profiler](https://github.com/idekerlab/cdgprofilergenestoterm), [Enrichr](https://github.com/idekerlab/cdenrichrgenestoterm), [iQuery](https://github.com/idekerlab/cdiquerygenestoterm) **If you use CyCommunityDetection in your research please cite:** Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, et al. (2020) Multiscale community detection in Cytoscape. PLoS Comput Biol 16(10): e1008239. https://doi.org/10.1371/journal.pcbi.1008239
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1.12.1

Works with Cytoscape 3.7

Release Notes

* For compatibility with CX and CX2 on NDEx, set value for ``CD_AnnotatedMembers_Pvalue`` to ``1.0`` instead of ``NaN`` when no pvalue is calculated. Also set value for ``CD_AnnotatedMembers_Overlap`` to ``0.0`` when no overlap is calculated.

1.12.0

Works with Cytoscape 3.7

Release Notes

* Added new menu option `Apps -> Community Detection -> Tally Attributes in Hierarchy` that annotates the hierarchy network by adding columns using values tallied from a set of attributes/columns in the parent network. * Order of algorithms displayed in **Run Community Detection** and **Run Functional Enrichment** dialogs are now consistent with what is returned from CDAPS REST server. UD-1573

1.11.0

Works with Cytoscape 3.7

Release Notes

* Added support for new edge list format COMMUNITYDETECTRESULTV2 allowing Community Detection algorithms to add additional custom node columns. UD-1091 Bug fixes * Fixed bug where `View Interactions for Selected Node` no longer worked if a session was reloaded. UD-1087 * Fixed bug where any values set in the community detection or functional enrichment dialogs were lost when when reopening those dialogs. [https://github.com/cytoscape/cy-community-detection/issues/3 Issue 3]

1.10.0

Works with Cytoscape 3.7

Release Notes

* Added new menu option `App -> Community Detection -> Settings` that lets caller easily change CDAPS REST server. UD-1066 * Added message letting user know using weight column in Community Detection dialog is an advanced parameter. UD-988 * In Community Detection dialog replaced **About** button with info icon next to algorithm selection dropdown. UD-987 Bug fixes * Fixed bug where changes to properties under `Edit -> Properties -> CyCommunityDetection` were not being loaded. UD-986

1.0

Works with Cytoscape 3.7

CYTOSCAPE 3

Version 1.12.1

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Released 5 Jan 2024

Works with Cytoscape 3.7

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