The article introduces NetworkAnalyzer, a versatile and user-friendly Java plugin for Cytoscape, designed to compute and display a comprehensive set of topological parameters for biological networks. These parameters include 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. NetworkAnalyzer supports both directed and undirected networks and offers additional functionalities such as constructing intersections or unions of networks. It is highly customizable and requires no expert knowledge in graph theory. The plugin is available for download from the Cytoscape website and has been validated against other tools like Pajek, TopNet, and NetworkX. The article also highlights novel network properties computed by NetworkAnalyzer, such as extended neighborhood connectivity for directed networks and the ability to enumerate shared neighbors. The tool's visual settings and node attribute storage allow for easy integration with Cytoscape's visualization capabilities, making it a valuable resource for analyzing biological networks.The article introduces NetworkAnalyzer, a versatile and user-friendly Java plugin for Cytoscape, designed to compute and display a comprehensive set of topological parameters for biological networks. These parameters include 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. NetworkAnalyzer supports both directed and undirected networks and offers additional functionalities such as constructing intersections or unions of networks. It is highly customizable and requires no expert knowledge in graph theory. The plugin is available for download from the Cytoscape website and has been validated against other tools like Pajek, TopNet, and NetworkX. The article also highlights novel network properties computed by NetworkAnalyzer, such as extended neighborhood connectivity for directed networks and the ability to enumerate shared neighbors. The tool's visual settings and node attribute storage allow for easy integration with Cytoscape's visualization capabilities, making it a valuable resource for analyzing biological networks.