This paper provides a comprehensive guide to the 152 publicly available Cytoscape plugins, covering their functionalities and distribution. Cytoscape is an open-source software for integrating, visualizing, and analyzing biological networks. The growth of Cytoscape plugins has been organic, driven by diverse authors, leading to a diverse and powerful set of tools. The paper describes the process of submitting, validating, and distributing plugins, as well as ongoing efforts to organize and maintain the collection. It also outlines the workflow of network analysis using Cytoscape, including network import, literature mining, network inference, topological analysis, clustering, functional enrichment, integration with other data, network comparison, and scripting. The authors highlight the importance of plugins in enhancing the functionality of Cytoscape and provide a classification system based on tags to help users find suitable plugins. Additionally, they discuss community resources and future directions, including the development of Cytoscape 3.0 and the Cytoscape AppStore.This paper provides a comprehensive guide to the 152 publicly available Cytoscape plugins, covering their functionalities and distribution. Cytoscape is an open-source software for integrating, visualizing, and analyzing biological networks. The growth of Cytoscape plugins has been organic, driven by diverse authors, leading to a diverse and powerful set of tools. The paper describes the process of submitting, validating, and distributing plugins, as well as ongoing efforts to organize and maintain the collection. It also outlines the workflow of network analysis using Cytoscape, including network import, literature mining, network inference, topological analysis, clustering, functional enrichment, integration with other data, network comparison, and scripting. The authors highlight the importance of plugins in enhancing the functionality of Cytoscape and provide a classification system based on tags to help users find suitable plugins. Additionally, they discuss community resources and future directions, including the development of Cytoscape 3.0 and the Cytoscape AppStore.