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| Name/platform | Description | Type | Webpage |
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| Cytoscape | An open source software platform for analyzing and visualizing complex networks: integrating a lot of plugins (Apps) concerning network analysis, communication scripting, and functional enrichment for biological network analysis. In addition, the package allows third-party developers to extend functionality of network analysis based on Java script [22, 23]. | Free | http://www.cytoscape.org/ |
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| Pajek | A particularly useful package for the analysis of very large networks: integrating many network analysis methods. Thanks to its specific.net data file type, most of the algorithms of network analysis run quickly and scale well [167]. | Free | http://pajek.imfm.si/doku.php |
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| NetworkX | A Python-based package for comprehensive analysis of complex networks: integrating many network analysis methods including network structure and analysis measures. | Free | http://networkx.github.io/ |
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| Ucinet | A comprehensive package for the analysis of network: providing many network analysis methods as well as multivariate statistics. In addition, the package has strong matrix analysis such as matrix algebra and can be used to analyze different mode network data. | Commercial use | http://www.analytictech.com/ucinet/ |
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| NetMiner | An application software for exploratory analysis and visualization of large network data: providing 73 kinds of network analysis modules, 25 kinds of statistic and mining analysis modules, 28 kinds of visualization algorithms, 21 kinds of data transform modules. | Commercial use | http://www.netminer.com/ |
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| Guess | An exploratory data analysis and visualization tool for graphs and networks supporting Python which facilitate to the researcher working on graph structures in their own manners. | Free | http://graphexploration.cond.org/ |
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| Complex Networks Package for Matlab | Providing a comprehensive framework for both static and dynamic network analysis in Matlab. | Free | http://www.levmuchnik.net/Content/Networks/ComplexNetworksPackage.html |
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| QuACN | An R Package for analyzing complex biological networks: providing function of analysis, classification and comparison for networks by different topological network descriptors [168, 169]. | Free | http://cran.r-project.org/web/packages/QuACN/ |
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