CytoCluster is a Cytoscape app for analysis and visualization of clusters from network, and has been tested on Cytoscape 3.0.X.
[https://drive.google.com/open?id=0B2lezDiMGuNoaUxZYVI0c2hDZTg Please downlaod the manual.]
###1. Introduction
CytoCluster is a Cytoscape app for analysis and visualization of clusters from network. Three different graph clustering algorithms (HC-PIN[1], OH-PIN[2], IPCA[3], ClusterONE[4], DCU[5], IPC-MCE[6], ) and BinGO were implemented in CytoCluster. This app is developed by Yu Tang and Dongyan Li directed by Dr. Jianxin Wang, Dr. Min Li and Dr.Jiancheng Zhong from Central South University.
###2. Quick Start
Following is a short quick start for the usage of CytoCluster, detailed information of the algorithms implemented in this plug-in can be found in related papers.
1. Start Cytoscape, install the CytoCluster.jar through App Manager(Apps → App Manager → Install from file..)
2. Import or open a network.
3. Click App → CytoCluster → Start CytoCluster.
4. It will switch to CytoCluster tab on left panel, choose the clustering algorithm and keep all parameters as default or you can customize the parameters as you want.
5. Click Analysis button.
6. After analysis is done, results will be shown in right panel. You can check the attributes of the selected cluster or export the results if you like. Results can be sorted by score or size or modularity.
###3. References
1. Wang J, Li M, Chen J, et al. A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks[J]. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 2011, 8(3): 607-620.
2. Wang J, Ren J, Li M, et al. Identification of Hierarchical and Overlapping Functional Modules in PPI Networks[J]. 2012.
3. Li M, Chen J, Wang J, et al. Modifying the DPClus algorithm for identifying protein complexes based on new topological structures[J]. Bmc Bioinformatics, 2008, 9(1): 398.
4. Nepusz T, Yu H, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks[J]. Nature methods, 2012, 9(5): 471-472.
5. Zhao B, Wang J, Li M, et al. Detecting protein complexes based on uncertain graph model[J]. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2014, 11(3): 486-497.
6. Li M, Wang J X, Liu B B, et al. An algorithm for identifying protein complexes based on maximal clique extension[J]. Journal of Central South University, 2010, 41(2): 560-565.
### 4. Citation
Please cite the following manuscript when you use CytoCluster:
<p> Min Li,Yu Tang, Dongyan Li,Fangxiang Wu, Jianxin Wang, **CytoCluster: a cytoscape plugin for cluster analysis and visualization of biological networks**
###5. Contact Information
If you have any problems or suggestions of CytoCluster, please contact us at Email: **limin@mail.csu.edu.cn**, **tangyu333@gmail.com**, **dongyanli@csu.edu.cn**, **faw341@mail.usask.ca**, **jxwang@mail.csu.edu.cn**.
<p>For more information please visit: [https://code.google.com/p/cytocluster-cytoscape/]
### 6. Related Tools
Our group also developed serveral related tools:
<p>**[http://apps.cytoscape.org/apps/cytonca CytoNCA]**
<p>Providing calculation, evaluation and visualization analysis for several centralities of weighted and unweighted network.
<p>**[http://apps.cytoscape.org/apps/clusterviz ClusterViz]**
<p>Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
<p>**[http://apps.cytoscape.org/apps/CytoCtrlAnalyser CytoCtrlAnalyser]**
<p>Integrated algorithms for the network control problem
<p>**[http://apps.cytoscape.org/apps/dynetviewer DyNetViewer ]**
<p>Constructing, analyzing, and visualizing dynamic networks.
