Table 3.

Cytoscape apps for networks and omics data.

Name	Description
Omnipath App	It allows access to the large collection of network resources of the Omnipath web server. From the 61 web resources the user can import any combination of networks and their respective annotations. The purpose of the app is to link the access to this kind of data to the Cytoscape functionalities [65].
Omics Visualizer	It is a data visualization app; it is ideal for omics data in which each node of the network is associated to multiple values. Indeed, the app allows the user to import files with multiple rows of data for a single node and offers different ways to visualize these data [66].
BiNGO	It is a Cytoscape plug-in of the Biological Networks Gene Ontology resource. It analyzes GO term enrichments and it maps them onto a given network, it uses either the full GO ontologies annotation or the GOSlim ontologies. The annotated graphs generated by BiNGO are flexible and customizable by the standard Cytoscape functionalities [67].
CytoCopteR	It is the graphical interface of CellNOptR. With this App the user can combine literature-derived network with experimental data to build and optimize cell specific and predictive logic networks. It uses different kind of logic formalisms (Boolean steady-state, Boolean multiple steady-state, Boolean time courses through synchronous update, steady-state constrained fuzzy logic and continuous logic-based ODEs) and the user can choose between them depending on the kind and the amount of data to analyze [68].