Non-programmatic options for large networksĪ non-programmatic option for handling large networks is Gephi (Figure 22). It is quite demanding in terms of computing resources when it comes to large-scale networks and it reaches a limit of what it can handle once networks become too large (hundreds of thousands of nodes and edges).Cytoscape tasks can be automated through command-line arguments, although the number of features you can access this way is still limited.It is important to check that you have the right version for the type of analysis you need to run Some Cytoscape apps will only work with a specific version of the core distribution of Cytoscape.For PPI network analysis there are specific apps for community search, (for example MCODE, clusterMaker2, JActiveModules) or to perform Gene Set Enrichment Analysis ( BiNGO, ClueGO, EnrichmentMap).This provides great flexibility, making the tool adaptable to multiple types of analysis in various domains of knowledge One of the main reasons for its popularity is the large variety of apps (almost 300 at the time we wrote this course) that provide further, specific functionality to the core distribution of Cytoscape.It was originally designed for the analysis of biological networks, which remains as its main application, but can also be used for general purpose network analysis. It is an open-source, Java-based, multi-platform desktop application that is widely used for network representation, integration and analysis (Figure 21). Assessing reliability and measuring confidenceĪll materials are free cultural works licensed under a Creative CommonsĪttribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.Ĭytoscape is one of the most popular network analysis tools.Network representation and analysis tools. ![]() Properties of PPINs: scale-free networks.Properties of PPINs: small world effect.The sources of data underlying biological networks.Graph theory: graph types and edge properties.
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