This article provides a comprehensive overview of Cytoscape plugins, which are extensions that enhance the functionality of Cytoscape, an open-source software for visualizing and analyzing biological networks. The authors present a guide to the 152 publicly available plugins for Cytoscape 2.5–2.8, highlighting their diversity and the ongoing efforts to organize and maintain them. The paper discusses the importance of these plugins in enabling researchers to analyze complex biological data, including protein-protein interactions, genetic interactions, and gene coexpression. It also describes the process of finding and installing plugins, as well as the validation of their functionality. The article covers various aspects of network analysis, including network import, literature mining, network inference, topological analysis, functional enrichment, and integration with other data types. It also discusses the development of plugins for scripting and programmatic access, as well as additional plugins that serve different purposes. The paper emphasizes the growing community of developers and users who contribute to the Cytoscape ecosystem, and outlines future directions for improving the platform and its plugins. The authors also highlight the importance of the Cytoscape community in advancing network biology research.This article provides a comprehensive overview of Cytoscape plugins, which are extensions that enhance the functionality of Cytoscape, an open-source software for visualizing and analyzing biological networks. The authors present a guide to the 152 publicly available plugins for Cytoscape 2.5–2.8, highlighting their diversity and the ongoing efforts to organize and maintain them. The paper discusses the importance of these plugins in enabling researchers to analyze complex biological data, including protein-protein interactions, genetic interactions, and gene coexpression. It also describes the process of finding and installing plugins, as well as the validation of their functionality. The article covers various aspects of network analysis, including network import, literature mining, network inference, topological analysis, functional enrichment, and integration with other data types. It also discusses the development of plugins for scripting and programmatic access, as well as additional plugins that serve different purposes. The paper emphasizes the growing community of developers and users who contribute to the Cytoscape ecosystem, and outlines future directions for improving the platform and its plugins. The authors also highlight the importance of the Cytoscape community in advancing network biology research.