NetworkAnalyzer is a user-friendly Java plugin for Cytoscape that computes and displays a comprehensive set of topological parameters for biological networks. It calculates parameters such as the number of nodes, edges, connected components, network diameter, radius, density, centralization, heterogeneity, clustering coefficient, characteristic path length, and distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. The plugin can be applied to both directed and undirected networks and allows the construction of the intersection or union of two networks. It is interactive and highly customizable, requiring no expert knowledge in graph theory. NetworkAnalyzer is available via the Cytoscape website and provides detailed information on all topological parameters in its online help. It compares its results with those from Pajek, TopNet, and NetworkX to ensure accuracy. The plugin extends the original definition of neighborhood connectivity to directed networks by introducing three types of related connectivity parameters. It also enumerates shared neighbors of all node pairs in a network, which can be used to detect bias in predicted human protein-protein interaction networks. NetworkAnalyzer offers various visual settings for displaying and exporting distributions as histograms, scatter plots, or chart images in formats like JPG/PNG/SVG. Users can customize the appearance of results by choosing between two interfaces. Topology parameters are stored as node attributes in Cytoscape, allowing users to visualize them proportionally to node size or color. The plugin also enables the selection of nodes based on calculated attributes, helping users examine structural perturbations in networks caused by the removal of high-degree nodes. NetworkAnalyzer computes a complete set of simple and complex parameters, referred to as network statistics, which can be saved and reloaded. It supports network modifications, including the construction of intersections, unions, and differences of networks, the extraction of connected components, and the removal of self-loops. The plugin is well integrated into Cytoscape and provides a comprehensive list of topology parameters using efficient graph algorithms. It incorporates useful visualization settings to display and export results and adds node attributes for the results.NetworkAnalyzer is a user-friendly Java plugin for Cytoscape that computes and displays a comprehensive set of topological parameters for biological networks. It calculates parameters such as the number of nodes, edges, connected components, network diameter, radius, density, centralization, heterogeneity, clustering coefficient, characteristic path length, and distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. The plugin can be applied to both directed and undirected networks and allows the construction of the intersection or union of two networks. It is interactive and highly customizable, requiring no expert knowledge in graph theory. NetworkAnalyzer is available via the Cytoscape website and provides detailed information on all topological parameters in its online help. It compares its results with those from Pajek, TopNet, and NetworkX to ensure accuracy. The plugin extends the original definition of neighborhood connectivity to directed networks by introducing three types of related connectivity parameters. It also enumerates shared neighbors of all node pairs in a network, which can be used to detect bias in predicted human protein-protein interaction networks. NetworkAnalyzer offers various visual settings for displaying and exporting distributions as histograms, scatter plots, or chart images in formats like JPG/PNG/SVG. Users can customize the appearance of results by choosing between two interfaces. Topology parameters are stored as node attributes in Cytoscape, allowing users to visualize them proportionally to node size or color. The plugin also enables the selection of nodes based on calculated attributes, helping users examine structural perturbations in networks caused by the removal of high-degree nodes. NetworkAnalyzer computes a complete set of simple and complex parameters, referred to as network statistics, which can be saved and reloaded. It supports network modifications, including the construction of intersections, unions, and differences of networks, the extraction of connected components, and the removal of self-loops. The plugin is well integrated into Cytoscape and provides a comprehensive list of topology parameters using efficient graph algorithms. It incorporates useful visualization settings to display and export results and adds node attributes for the results.