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Cytoscape Desktop Apps

	ExpressionCorrelation
	Makes a similarity network where nodes are genes, and edges denote highly correlated genes.

	ExpressionCorrelation
	Makes a similarity network where nodes are genes, and edges denote highly correlated genes.
	(5) 13489 downloads

	AgilentLiteratureSearch
	Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.

	AgilentLiteratureSearch
	Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
	(28) 72728 downloads

	MetScape
	Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.

	MetScape
	Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
	(25) 67975 downloads

	PiNGO
	Finds candidate genes in a network that are associated with user-defined target GO terms.

	PiNGO
	Finds candidate genes in a network that are associated with user-defined target GO terms.
	(4) 6553 downloads

	KeyPathwayMiner
	Detects highly-connected sub-networks where most genes show similar expression behavior.

	KeyPathwayMiner
	Detects highly-connected sub-networks where most genes show similar expression behavior.
	(70) 25791 downloads

	CentiScaPe
	Find the most important nodes in a network, calculating centrality parameters for each node.

	CentiScaPe
	Find the most important nodes in a network, calculating centrality parameters for each node.
	(40) 73278 downloads

	cytoHubba
	Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.

	cytoHubba
	Predicts and explores important nodes and subnetworks in a given network by several topological algorithms.
	(171) 213369 downloads

	EnrichmentMap
	Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.

	EnrichmentMap
	Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
	(29) 169643 downloads

	PanGIA
	Integrated analysis and visualization of physical and genetic interactions to infer genetic module maps

	PanGIA
	Integrated analysis and visualization of physical and genetic interactions to infer genetic module maps
	(0) 3860 downloads

	RINalyzer
	Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).

	RINalyzer
	Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).
	(9) 9049 downloads

	CytoCopteR
	A Cytoscape plug-in for training logic models

	CytoCopteR
	A Cytoscape plug-in for training logic models
	(29) 14392 downloads

	DynNetwork
	Visualize dynamic networks in Cytoscape 3.0

	DynNetwork
	Visualize dynamic networks in Cytoscape 3.0
	(13) 27565 downloads

	Cy3 Performance Reporter
	A diagnostics tool for collecting information about Cytoscape 3 performance. Requires Cy3 beta2-SNAPSHOT or later. Doesn't work with beta1.

	Cy3 Performance Reporter
	A diagnostics tool for collecting information about Cytoscape 3 performance. Requires Cy3 beta2-SNAPSHOT or later. Doesn't work with beta1.
	(0) 6626 downloads

	PathExplorer
	Finds paths, filters them based on node and edge attributes and saves them.

	PathExplorer
	Finds paths, filters them based on node and edge attributes and saves them.
	(41) 16025 downloads

	Cyni Toolbox
	Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)

	Cyni Toolbox
	Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
	(25) 23837 downloads

	SemScape
	Visualizes Semantic Data Landscapes

	SemScape
	Visualizes Semantic Data Landscapes
	(36) 7482 downloads

	CytoCluster
	a Cytoscape app for analysis and visualization of clusters from network

	CytoCluster
	a Cytoscape app for analysis and visualization of clusters from network
	(12) 43277 downloads

	WikiPathways
	WikiPathways web service client and GPML file format importer

	WikiPathways
	WikiPathways web service client and GPML file format importer
	(11) 110285 downloads

	ENViz
	Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation

	ENViz
	Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation
	(14) 42356 downloads

	PEPPER
	Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization

	PEPPER
	Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
	(44) 32700 downloads

	GenomeSpace
	Enables communication with GenomeSpace

	GenomeSpace
	Enables communication with GenomeSpace
	(5) 9326 downloads

	iRegulon
	Detects master regulators and cis-regulatory interactions

	iRegulon
	Detects master regulators and cis-regulatory interactions
	(12) 39488 downloads

	eXamine
	A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.

	eXamine
	A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
	(34) 25459 downloads

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
	(1) 6444 downloads

	GASOLINE
	A Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks

	GASOLINE
	A Cytoscape App for multiple local alignment of protein-protein interaction (PPI) networks
	(13) 14333 downloads

	KEGGscape
	File reader and pathway visualizer for KEGG XML (KGML) files

	KEGGscape
	File reader and pathway visualizer for KEGG XML (KGML) files
	(4) 111552 downloads

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape
	(28) 179910 downloads

	setsApp
	Save and manipulate sets of nodes and edges

	setsApp
	Save and manipulate sets of nodes and edges
	(3) 23266 downloads

	D3.js Exporter
	Network and Table Data Exporter for D3.js

	D3.js Exporter
	Network and Table Data Exporter for D3.js
	(1) 15748 downloads

	KDDN
	Knowledge-fused Differential Dependency Network

	KDDN
	Knowledge-fused Differential Dependency Network
	(7) 8015 downloads

	Rene
	Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit

	Rene
	Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
	(12) 42176 downloads

	Synapse Client
	Access your data on Synapse.org from within Cyoscape

	Synapse Client
	Access your data on Synapse.org from within Cyoscape
	(1) 6708 downloads

	structureViz2
	App to visualize macromolecular structures in a network context

	structureViz2
	App to visualize macromolecular structures in a network context
	(4) 17295 downloads

	Propagate

	Propagate

	(0) 2656 downloads

	CyNetworkBMA
	Infers gene regulatory networks from expression measurements using Bayesian Model Averaging.

	CyNetworkBMA
	Infers gene regulatory networks from expression measurements using Bayesian Model Averaging.
	(1) 4779 downloads

	JGF App
	Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.

	JGF App
	Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.
	(1) 9487 downloads

	cyREST
	Core App: Language-agnostic RESTful API

	cyREST
	Core App: Language-agnostic RESTful API
	(4) 162125 downloads

	ThematicMap
	ThematicMap visualizes the relationships between node attributes. It can help simplify complex networks and highlight hidden relationships.

	ThematicMap
	ThematicMap visualizes the relationships between node attributes. It can help simplify complex networks and highlight hidden relationships.
	(0) 5496 downloads

	EntOptLayout
	Relative entropy optimization based layout plugin

	EntOptLayout
	Relative entropy optimization based layout plugin
	(6) 14567 downloads

	cyNeo4j
	A Cytoscape app to connect to a Neo4j database and execute extensions of the Neo4j database.

	cyNeo4j
	A Cytoscape app to connect to a Neo4j database and execute extensions of the Neo4j database.
	(11) 10397 downloads

	ModuLand 2.0
	Modularization method family offering modular hierarchies and adjustable overlaps

	ModuLand 2.0
	Modularization method family offering modular hierarchies and adjustable overlaps
	(2) 10787 downloads

	General SPARQL
	Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF

	General SPARQL
	Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF
	(10) 22432 downloads

	CyAnimator
	Simple key-frame animation for Cytoscape

	CyAnimator
	Simple key-frame animation for Cytoscape
	(5) 52256 downloads

	CytoGEDEVO
	Pairwise global alignment of PPI or other networks

	CytoGEDEVO
	Pairwise global alignment of PPI or other networks
	(43) 15549 downloads

	cy3sbml
	cy3sbml visualizes SBML models (Systems Biology Markup Language)

	cy3sbml
	cy3sbml visualizes SBML models (Systems Biology Markup Language)
	(3) 41774 downloads

	Pesca3.0

	Pesca3.0

	(9) 6073 downloads

	SocialNetwork
	Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.

	SocialNetwork
	Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.
	(5) 15702 downloads

	Adj Exporter
	Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks

	Adj Exporter
	Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks
	(12) 14969 downloads

	dot-app
	Import/export of Graphviz files in Cytoscape

	dot-app
	Import/export of Graphviz files in Cytoscape
	(31) 20813 downloads

	Obfuscator
	Replaces names of nodes in one or more networks with random names, while preserving correspondence across networks.

	Obfuscator
	Replaces names of nodes in one or more networks with random names, while preserving correspondence across networks.
	(1) 7778 downloads

	Command Line Implementation
	Core App: Provides Cytoscape's Command Line Dialog tool

	Command Line Implementation
	Core App: Provides Cytoscape's Command Line Dialog tool
	(1) 10752 downloads

	Network Merge
	Core App: Provides Cytoscape's Network Merge tool

	Network Merge
	Core App: Provides Cytoscape's Network Merge tool
	(1) 46748 downloads

	OpenCL Prefuse Layout
	Core App: Provides faster OpenCL-based version of Cytoscape Prefuse layout

	OpenCL Prefuse Layout
	Core App: Provides faster OpenCL-based version of Cytoscape Prefuse layout
	(0) 30263 downloads

	SBML Reader
	Core App: Provides support for reading SBML files in Cytoscape

	SBML Reader
	Core App: Provides support for reading SBML files in Cytoscape
	(1) 20889 downloads

	PSICQUIC Web Service Client
	Core App: Provides support for PSICQUIC web service in Cytoscape

	PSICQUIC Web Service Client
	Core App: Provides support for PSICQUIC web service in Cytoscape
	(1) 10263 downloads

	cyTransFinder
	Signal Transduction Pathway Finder

	cyTransFinder
	Signal Transduction Pathway Finder
	(3) 30266 downloads

	Cy3D
	Simple 3D Network Renderer App

	Cy3D
	Simple 3D Network Renderer App
	(3) 24393 downloads

	layoutSaver
	Map node positions from one network to another

	layoutSaver
	Map node positions from one network to another
	(1) 5619 downloads

	SIREN
	Signing of Regulatory Networks

	SIREN
	Signing of Regulatory Networks
	(3) 4283 downloads

	Mclique
	Maximal Cliques in a given Cytoscape network, sorted by size

	Mclique
	Maximal Cliques in a given Cytoscape network, sorted by size
	(16) 13822 downloads

	CyIsomorphism
	All possible subgraph isomorphisms

	CyIsomorphism
	All possible subgraph isomorphisms
	(4) 6150 downloads

	Vital AI Graph Visualization
	Use Vital AI software to connect to Databases, Servers, and Hadoop/Spark

	Vital AI Graph Visualization
	Use Vital AI software to connect to Databases, Servers, and Hadoop/Spark
	(7) 11943 downloads

	NetMatchStar
	An enhanced Cytoscape network querying app

	NetMatchStar
	An enhanced Cytoscape network querying app
	(3) 11371 downloads

	CoExpNetViz
	Create a co-expression network between a subset of genes and all other genes of 1 or more species, grouping nodes by gene family.

	CoExpNetViz
	Create a co-expression network between a subset of genes and all other genes of 1 or more species, grouping nodes by gene family.
	(1) 16190 downloads

	AutoAnnotate
	Finds clusters and visually annotates them with labels and groups.

	AutoAnnotate
	Finds clusters and visually annotates them with labels and groups.
	(37) 79326 downloads

	CyNDEx
	CyNDEx allows users to seamlessly transfer networks between NDEx and Cytoscape as well as perform network updates in NDEx.

	CyNDEx
	CyNDEx allows users to seamlessly transfer networks between NDEx and Cytoscape as well as perform network updates in NDEx.
	(8) 11269 downloads

	TiCoNE
	Time Course Network Enricher is an interactive clustering method for time-series data

	TiCoNE
	Time Course Network Enricher is an interactive clustering method for time-series data
	(73) 64167 downloads

	Functional Enrichment Collection
	Collection of apps to facilitate functional enrichment analysis. By installing this app, you will be installing a set of apps.

	Functional Enrichment Collection
	Collection of apps to facilitate functional enrichment analysis. By installing this app, you will be installing a set of apps.
	(5) 37940 downloads

	JSON Support
	Core App: Provides support for reading/writing Cytoscape.js JSON files in Cytoscape

	JSON Support
	Core App: Provides support for reading/writing Cytoscape.js JSON files in Cytoscape
	(1) 18537 downloads

	EnrichmentMap Pipeline Collection
	Collection of Apps that are part of the EnrichmentMap pipeline workflow

	EnrichmentMap Pipeline Collection
	Collection of Apps that are part of the EnrichmentMap pipeline workflow
	(3) 30547 downloads

	SiGNetApp
	A Cytoscape App for producing network inference benchmarking data

	SiGNetApp
	A Cytoscape App for producing network inference benchmarking data
	(0) 2610 downloads

	PEmeasure
	Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)

	PEmeasure
	Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)
	(10) 4182 downloads

	CX Support
	Core App: CX JSON file reader and writer

	CX Support
	Core App: CX JSON file reader and writer
	(3) 100285 downloads

	CycleDetector
	Detects Cycles in a Cytoscape network

	CycleDetector
	Detects Cycles in a Cytoscape network
	(0) 4252 downloads

	ISMAGS
	Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.

	ISMAGS
	Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
	(1) 14198 downloads

	Motif-Discovery
	It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.

	Motif-Discovery
	It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
	(15) 14115 downloads

	PEWCC
	Detect dense sub-network (e.g. protein/gene complexes) in network (e.g. PPI/gene network)

	PEWCC
	Detect dense sub-network (e.g. protein/gene complexes) in network (e.g. PPI/gene network)
	(8) 4101 downloads

	WikiDataScape
	A WikiData explorer for Cytoscape

	WikiDataScape
	A WikiData explorer for Cytoscape
	(3) 11490 downloads

	CompleteGraph
	Creates a new fully connected Cytoscape network of given size

	CompleteGraph
	Creates a new fully connected Cytoscape network of given size
	(6) 4732 downloads

	GNC
	Gene Network Coherence with direct and indirect relationships

	GNC
	Gene Network Coherence with direct and indirect relationships
	(60) 9020 downloads

	CyFinder

	CyFinder

	(3) 5308 downloads

	CyNetSVM
	A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines

	CyNetSVM
	A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines
	(3) 3841 downloads

	CyDataSeries
	Add time series and the like to your networks.

	CyDataSeries
	Add time series and the like to your networks.
	(1) 9162 downloads

	Diffusion
	Expand node selection using network propagation algorithms

	Diffusion
	Expand node selection using network propagation algorithms
	(35) 41267 downloads

	CyGenexpi
	Uncover regulatory interactions from time course data

	CyGenexpi
	Uncover regulatory interactions from time course data
	(1) 11828 downloads

	FileWatcher
	An App to Link Networks with Excel Files

	FileWatcher
	An App to Link Networks with Excel Files
	(0) 5018 downloads

	EClerize

	EClerize

	(2) 2415 downloads

	PathInsight
	An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation

	PathInsight
	An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
	(1) 4044 downloads

	ID Mapper
	A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.

	ID Mapper
	A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.
	(1) 20460 downloads

	AOPXplorer

	AOPXplorer

	(0) 3301 downloads

	TMM
	Assess the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways

	TMM
	Assess the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways
	(0) 14493 downloads

	HGPEC
	HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization

	HGPEC
	HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
	(2) 4504 downloads

	CyLinkPredictor
	Link Predictor Based on Common Neighbors

	CyLinkPredictor
	Link Predictor Based on Common Neighbors
	(3) 3209 downloads

	polyLayout
	Simple n-partide layout algorithm that organizes categories along sides of regular polygons

	polyLayout
	Simple n-partide layout algorithm that organizes categories along sides of regular polygons
	(1) 5150 downloads

	CoordinatesLayout
	Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).

	CoordinatesLayout
	Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
	(9) 6058 downloads

	copycatLayout
	Clone a network view layout by mapping node column values

	copycatLayout
	Clone a network view layout by mapping node column values
	(1) 14563 downloads

	Cytoscape Neo4j Plugin

	Cytoscape Neo4j Plugin

	(5) 14472 downloads

	MORO

	MORO

	(1) 2545 downloads

	CountTriplets
	Counts graph triplets and plots significance profiles

	CountTriplets
	Counts graph triplets and plots significance profiles
	(1) 2930 downloads

	CyGraphSpace
	Upload Cytoscape networks to GraphSpace

	CyGraphSpace
	Upload Cytoscape networks to GraphSpace
	(3) 5638 downloads

	Pathway Studio Importer
	Import Relation Table CSV files output by Pathway Studio

	Pathway Studio Importer
	Import Relation Table CSV files output by Pathway Studio
	(1) 4121 downloads

	GRNCOP2
	Model-free combinatorial optimization algorithm to infer time-delayed gene regulatory networks from genome-wide time series datasets.

	GRNCOP2
	Model-free combinatorial optimization algorithm to infer time-delayed gene regulatory networks from genome-wide time series datasets.
	(4) 3081 downloads

	cyTRON

	cyTRON

	(0) 2153 downloads

	Cytoscape RedisGraph Plugin

	Cytoscape RedisGraph Plugin

	(1) 4457 downloads

	Legend Creator
	A way to add legends of discrete and continuous mappings to your graph

	Legend Creator
	A way to add legends of discrete and continuous mappings to your graph
	(5) 35287 downloads

	Omics Visualizer
	Import & Visualize several data for the same node

	Omics Visualizer
	Import & Visualize several data for the same node
	(10) 24163 downloads

	wk-shell-decomposition
	Performs a weighted k-shell decomposition

	wk-shell-decomposition
	Performs a weighted k-shell decomposition
	(1) 3994 downloads

	cyPlot
	A utility to display data plots

	cyPlot
	A utility to display data plots
	(1) 50726 downloads

	CyPathia
	Mechanistic models of pathways for omics data interpretation and analysis

	CyPathia
	Mechanistic models of pathways for omics data interpretation and analysis
	(3) 2793 downloads

	OCSANA+
	Optimal Control and Simulation of Signaling Networks from Network Analysis

	OCSANA+
	Optimal Control and Simulation of Signaling Networks from Network Analysis
	(27) 3675 downloads

	ZDOG

	ZDOG

	(0) 2207 downloads

	BioGateway Cytoscape Plugin
	An explorative network building plugin that works with the BioGateway triple store

	BioGateway Cytoscape Plugin
	An explorative network building plugin that works with the BioGateway triple store
	(8) 13610 downloads

	YoshikoStandalone
	Heuristic algorithms for weighted (k) cluster-editing. Works with Cytoscape 3.7.

	YoshikoStandalone
	Heuristic algorithms for weighted (k) cluster-editing. Works with Cytoscape 3.7.
	(4) 3342 downloads

	IntAct App
	Build molecular interaction networks from IntAct database. Access all details in one click.

	IntAct App
	Build molecular interaction networks from IntAct database. Access all details in one click.
	(7) 18391 downloads

	CONAN
	Analysis of atom interaction networks for structure ensembles of biomolecules

	CONAN
	Analysis of atom interaction networks for structure ensembles of biomolecules
	(1) 5259 downloads

	XlinkCyNET
	Generate residue-to-residue connections provided by XL-MS in protein interaction networks

	XlinkCyNET
	Generate residue-to-residue connections provided by XL-MS in protein interaction networks
	(4) 30703 downloads

	SenseNet
	Analysis of atom interaction networks for structure ensembles of biomolecules

	SenseNet
	Analysis of atom interaction networks for structure ensembles of biomolecules
	(1) 7297 downloads

	IDARE
	Data Visualisation for Multi-Omics data

	IDARE
	Data Visualisation for Multi-Omics data
	(0) 4207 downloads

	MSClustering
	an efficient app for hierarchical clustering and phylogenetics of complex networks

	MSClustering
	an efficient app for hierarchical clustering and phylogenetics of complex networks
	(55) 5013 downloads

	causalpath-cytoscape-app
	Visualize CausalPath (causalpath.org) results in Cytoscape

	causalpath-cytoscape-app
	Visualize CausalPath (causalpath.org) results in Cytoscape
	(2) 5052 downloads

	Signor App
	SIGNORApp is a Cytoscape 3 application that provides access to causal interactions data annotated in the SIGNOR resource. It builds networks

	Signor App
	SIGNORApp is a Cytoscape 3 application that provides access to causal interactions data annotated in the SIGNOR resource. It builds networks
	(2) 5383 downloads

	Network Coherence Calculator
	Calculates the network coherence of differentially expressed genes within a network.

	Network Coherence Calculator
	Calculates the network coherence of differentially expressed genes within a network.
	(3) 3735 downloads

	Arena3DwebApp
	Visualize a 2D network as a multilayered 3D network in Arena3Dweb

	Arena3DwebApp
	Visualize a 2D network as a multilayered 3D network in Arena3Dweb
	(2) 2523 downloads

	mapSourceAndTarget

	mapSourceAndTarget

	(2) 2098 downloads

	ColorCodingApp

	ColorCodingApp

	(0) 858 downloads

	ScyNet
	Visualisation of community metabolic models

	ScyNet
	Visualisation of community metabolic models
	(1) 2108 downloads

	CytoDiVR
	Dive into your Cytoscape networks in Virtual Reality

	CytoDiVR
	Dive into your Cytoscape networks in Virtual Reality
	(0) 1015 downloads

	ClustnSee 3
	clustering, module exploration and annotation

	ClustnSee 3
	clustering, module exploration and annotation
	(1) 1522 downloads

	FunCoup
	Import and analyze Cytoscape networks from FunCoup

	FunCoup
	Import and analyze Cytoscape networks from FunCoup
	(10) 3046 downloads

	SocialViruses
	SocialViruses app finds the best virus cocktails in terms of host range and virulence while reducing redundancy and antagonism.

	SocialViruses
	SocialViruses app finds the best virus cocktails in terms of host range and virulence while reducing redundancy and antagonism.
	(5) 466 downloads

	SAP HANA plug-in for Cytoscape
	Connect Cytoscape and SAP HANA to enable import, export and visualization of graph data stored in SAP HANA.

	SAP HANA plug-in for Cytoscape
	Connect Cytoscape and SAP HANA to enable import, export and visualization of graph data stored in SAP HANA.
	(1) 201 downloads

	GeneMANIA
	Imports interaction networks from public databases from a list of genes with their annotations and putative functions.

	GeneMANIA
	Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
	(80) 144488 downloads

	Bisogenet
	Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.

	Bisogenet
	Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
	(15) 83164 downloads

	BiNGO
	Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.

	BiNGO
	Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.
	(78) 203891 downloads

	ClueGO
	Creates and visualizes a functionally grouped network of terms/pathways

	ClueGO
	Creates and visualizes a functionally grouped network of terms/pathways
	(318) 406425 downloads

	ClusterViz
	Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.

	ClusterViz
	Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
	(13) 26007 downloads

	NetworkAnalyzer
	Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)

	NetworkAnalyzer
	Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)
	(12) 81541 downloads

	jActiveModules
	Finds clusters where member nodes show significant changes in expression levels.

	jActiveModules
	Finds clusters where member nodes show significant changes in expression levels.
	(36) 67360 downloads

	WordCloud
	Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.

	WordCloud
	Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
	(2) 75986 downloads

	Venn and Euler Diagrams
	Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.

	Venn and Euler Diagrams
	Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
	(36) 28107 downloads

	CyTargetLinker
	Flexible network extension app

	CyTargetLinker
	Flexible network extension app
	(40) 52260 downloads

	CyPath2
	Pathway Commons (BioPAX L3 database) web service GUI client app

	CyPath2
	Pathway Commons (BioPAX L3 database) web service GUI client app
	(73) 44073 downloads

	CluePedia
	CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data

	CluePedia
	CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
	(104) 234351 downloads

	Cyrface
	Bridging Cytoscape with R

	Cyrface
	Bridging Cytoscape with R
	(7) 6306 downloads

	SLiMScape
	A Protein Short Linear Motif Analysis Plugin for Cytoscape

	SLiMScape
	A Protein Short Linear Motif Analysis Plugin for Cytoscape
	(12) 15825 downloads

	GFD-Net
	Analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity

	GFD-Net
	Analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity
	(55) 20366 downloads

	JEPETTO
	Performs human gene set enrichment and topological analysis based on interaction networks.

	JEPETTO
	Performs human gene set enrichment and topological analysis based on interaction networks.
	(32) 23837 downloads

	CytoNCA
	Providing calculation, evaluation and visualization analysis for several centralities of weighted and unweighted network.

	CytoNCA
	Providing calculation, evaluation and visualization analysis for several centralities of weighted and unweighted network.
	(9) 134838 downloads

	PINA4MS
	Combining tissue-specific protein expression and interaction data to identify genes of functional- and disease-relevance

	PINA4MS
	Combining tissue-specific protein expression and interaction data to identify genes of functional- and disease-relevance
	(14) 17000 downloads

	ReactomeFIPlugIn
	Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network

	ReactomeFIPlugIn
	Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
	(23) 142541 downloads

	CoNet
	CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices.

	CoNet
	CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices.
	(22) 45646 downloads

	GIANT
	a Cytoscape plugin for network cartography

	GIANT
	a Cytoscape plugin for network cartography
	(1) 7566 downloads

	Pathway Scoring Application
	Evaluates the biological activity of genes and processes in pathways

	Pathway Scoring Application
	Evaluates the biological activity of genes and processes in pathways
	(2) 10559 downloads

	MetDisease
	Annotates metabolic networks with MeSH disease terms and links to references.

	MetDisease
	Annotates metabolic networks with MeSH disease terms and links to references.
	(5) 11239 downloads

	CyKEGGParser
	KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways

	CyKEGGParser
	KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
	(14) 66119 downloads

	enhancedGraphics
	A passthrough mapper for charts and gradients

	enhancedGraphics
	A passthrough mapper for charts and gradients
	(11) 169323 downloads

	bayelviraApp
	Learning and generation of Bayesian networks.

	bayelviraApp
	Learning and generation of Bayesian networks.
	(1) 5232 downloads

	chemViz2
	Cheminformatics App for Cytoscape

	chemViz2
	Cheminformatics App for Cytoscape
	(8) 32469 downloads

	Worm Plot
	Sequence self-similarity directed graph visualization.

	Worm Plot
	Sequence self-similarity directed graph visualization.
	(0) 12758 downloads

	BridgeDb
	Performs ID mapping using BridgeDb and other public or custom database sources.

	BridgeDb
	Performs ID mapping using BridgeDb and other public or custom database sources.
	(20) 21752 downloads

	Variation
	Integrate variation and variation consequence data on biological networks.

	Variation
	Integrate variation and variation consequence data on biological networks.
	(0) 4290 downloads

	CyLineUp
	Visualizes data in network small multiples

	CyLineUp
	Visualizes data in network small multiples
	(2) 8748 downloads

	PetriScape
	PetriScape performs discrete simulation of Petri Nets and also convert SBML files into the Petri Net formalism.

	PetriScape
	PetriScape performs discrete simulation of Petri Nets and also convert SBML files into the Petri Net formalism.
	(29) 4206 downloads

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database
	(0) 16394 downloads

	CyToStruct: external application hooking
	Launching arbitrary external apps (such as viewers) for nodes/edges

	CyToStruct: external application hooking
	Launching arbitrary external apps (such as viewers) for nodes/edges
	(27) 28560 downloads

	ARACNE
	Network inference algorithm to address a wide range of network deconvolution problems available through Cyni

	ARACNE
	Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
	(10) 13178 downloads

	PINBPA
	Protein-interaction-network-based Pathway Analysis

	PINBPA
	Protein-interaction-network-based Pathway Analysis
	(5) 18230 downloads

	GOlorize
	Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.

	GOlorize
	Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.
	(2) 16662 downloads

	ANIMO
	ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.

	ANIMO
	ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.
	(1) 49526 downloads

	CytoAsp

	CytoAsp

	(0) 3508 downloads

	RenoDoI
	A visual analytics approach for integrated data-knowledge networks.

	RenoDoI
	A visual analytics approach for integrated data-knowledge networks.
	(1) 4723 downloads

	ncINetView

	ncINetView

	(0) 3336 downloads

	AnatApp
	Elucidating functional networks of proteins

	AnatApp
	Elucidating functional networks of proteins
	(1) 5246 downloads

	SCODE
	This is the Cytoscape app implementation for Protein Complex Identification by Supervised Graph Clustering

	SCODE
	This is the Cytoscape app implementation for Protein Complex Identification by Supervised Graph Clustering
	(0) 13817 downloads

	Strongest Path
	An application for protein-protein interaction analysis

	Strongest Path
	An application for protein-protein interaction analysis
	(25) 10819 downloads

	CySpanningTree
	Spanning tree computation and MST heuristic for Travelling Salesman Problem

	CySpanningTree
	Spanning tree computation and MST heuristic for Travelling Salesman Problem
	(5) 7669 downloads

	PSFC
	Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.

	PSFC
	Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
	(1) 26083 downloads

	PTMOracle
	Co-visualisation and co-analysis of PTM and PPI data

	PTMOracle
	Co-visualisation and co-analysis of PTM and PPI data
	(4) 10646 downloads

	PhosphoPath
	Visualization and analysis of quantitative proteome and phosphoproteome datasets

	PhosphoPath
	Visualization and analysis of quantitative proteome and phosphoproteome datasets
	(17) 30366 downloads

	TieDIE
	Tied Diffusion Through Interacting Events

	TieDIE
	Tied Diffusion Through Interacting Events
	(1) 6478 downloads

	BioPAX Reader
	Core App: Provides support for reading BioPAX files in Cytoscape

	BioPAX Reader
	Core App: Provides support for reading BioPAX files in Cytoscape
	(41) 17271 downloads

	BioGRID Data Source
	Core App: Provides support for BioGRID data in Cytoscape

	BioGRID Data Source
	Core App: Provides support for BioGRID data in Cytoscape
	(2) 13437 downloads

	CyCL
	Core App: Provides OpenCL support for Cytoscape

	CyCL
	Core App: Provides OpenCL support for Cytoscape
	(0) 32254 downloads

	PSI-MI Reader
	Core App: Provides support for reading PSI-MI files in Cytoscape

	PSI-MI Reader
	Core App: Provides support for reading PSI-MI files in Cytoscape
	(0) 11442 downloads

	Biomart Web Service Client
	Core App: Provides support for Biomart web service in Cytoscape

	Biomart Web Service Client
	Core App: Provides support for Biomart web service in Cytoscape
	(0) 12309 downloads

	Welcome Screen
	Core App: Provides Cytoscape welcome screen

	Welcome Screen
	Core App: Provides Cytoscape welcome screen
	(0) 14153 downloads

	aMatReader
	App to read adjacency matrix (.mat, .adj) files

	aMatReader
	App to read adjacency matrix (.mat, .adj) files
	(2) 17656 downloads

	cdtReader
	Read Cluster 3 output files into Cytoscape

	cdtReader
	Read Cluster 3 output files into Cytoscape
	(0) 5948 downloads

	stringApp
	Import and augment Cytoscape networks from STRING

	stringApp
	Import and augment Cytoscape networks from STRING
	(34) 391191 downloads

	PathLinker
	Reconstructs signaling pathways from protein interaction networks

	PathLinker
	Reconstructs signaling pathways from protein interaction networks
	(14) 33268 downloads

	Diffany
	Calculation of differential networks

	Diffany
	Calculation of differential networks
	(4) 4359 downloads

	NCMine
	Finds functional modules in gene networks by Near-Clique Mining

	NCMine
	Finds functional modules in gene networks by Near-Clique Mining
	(3) 4768 downloads

	DyNet
	Compare two or more networks and identify the most 'rewired' nodes.

	DyNet
	Compare two or more networks and identify the most 'rewired' nodes.
	(7) 15509 downloads

	MCDS
	Approximates the minimum connected dominating set (MCDS) of directed networks.

	MCDS
	Approximates the minimum connected dominating set (MCDS) of directed networks.
	(14) 6956 downloads

	Omics Analysis Collection
	Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.

	Omics Analysis Collection
	Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.
	(1) 26551 downloads

	RNA
	Regulatory Network Analyzer generates/analyzes a regulatory network and states transition network and computes informations like entropy.

	RNA
	Regulatory Network Analyzer generates/analyzes a regulatory network and states transition network and computes informations like entropy.
	(2) 14623 downloads

	science-direct
	Assists in preparing network for submission to journals having an interactive network viewer

	science-direct
	Assists in preparing network for submission to journals having an interactive network viewer
	(0) 5901 downloads

	gexf-app
	Imports Graph Exchange XML Format (GEXF) files

	gexf-app
	Imports Graph Exchange XML Format (GEXF) files
	(1) 7956 downloads

	Mass Spec Collection
	Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.

	Mass Spec Collection
	Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.
	(3) 18903 downloads

	Core Apps
	Core App: Set of apps packaged with the regular Cytoscape distribution. You do not need to install these separately.

	Core Apps
	Core App: Set of apps packaged with the regular Cytoscape distribution. You do not need to install these separately.
	(1) 4587 downloads

	DeDaL
	Data-driven layout (PCA...), network alignement, network morphing.

	DeDaL
	Data-driven layout (PCA...), network alignement, network morphing.
	(1) 6115 downloads

	cy3sabiork
	SABIO-RK webservice access

	cy3sabiork
	SABIO-RK webservice access
	(1) 12217 downloads

	NetworksInfo-writer
	Writes information about all networks of control panel in a .csv file

	NetworksInfo-writer
	Writes information about all networks of control panel in a .csv file
	(0) 3599 downloads

	Network Randomizer
	A tool for creating random networks and comparing them to the real ones

	Network Randomizer
	A tool for creating random networks and comparing them to the real ones
	(5) 17546 downloads

	CHAT
	Identify contextually relevant hubs in biological networks

	CHAT
	Identify contextually relevant hubs in biological networks
	(2) 22347 downloads

	BEL Navigator
	Explore OpenBEL knowledge networks within Cytoscape 3.

	BEL Navigator
	Explore OpenBEL knowledge networks within Cytoscape 3.
	(0) 3279 downloads

	SDP Model Builder
	Cytoscape 3 app that interfaces with Selventa Development Platform

	SDP Model Builder
	Cytoscape 3 app that interfaces with Selventa Development Platform
	(0) 2822 downloads

	DisGeNET-app
	Query, analyze, and visualize DISGENET data

	DisGeNET-app
	Query, analyze, and visualize DISGENET data
	(9) 77903 downloads

	PhenomeScape
	identify differentially regulated sub-networks from gene expression data using known disease associations

	PhenomeScape
	identify differentially regulated sub-networks from gene expression data using known disease associations
	(4) 15460 downloads

	NDB Reader
	Cytoscape app for reading Genomica NDB files

	NDB Reader
	Cytoscape app for reading Genomica NDB files
	(0) 2900 downloads

	netIMP
	Visualize IMP pathway models

	netIMP
	Visualize IMP pathway models
	(0) 2421 downloads

	Color Cast
	Applies a Brewer Color Palette to Network Nodes

	Color Cast
	Applies a Brewer Color Palette to Network Nodes
	(7) 8558 downloads

	SAFE
	Spatial Analysis for Functional Enrichment

	SAFE
	Spatial Analysis for Functional Enrichment
	(0) 8759 downloads

	DyNetViewer
	Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0

	DyNetViewer
	Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
	(4) 13520 downloads

	CytoGTA
	Module (cluster) detection in PPI network based on gene expressions

	CytoGTA
	Module (cluster) detection in PPI network based on gene expressions
	(31) 6806 downloads

	Orthoscape
	Orthoscape aimed to analyze evolutionary information in the gene networks and gene sets

	Orthoscape
	Orthoscape aimed to analyze evolutionary information in the gene networks and gene sets
	(4) 18157 downloads

	PCM
	Assemble Predicted Clusters For better Proteins Cluster Detection

	PCM
	Assemble Predicted Clusters For better Proteins Cluster Detection
	(4) 3100 downloads

	CytoMCS
	Computes the maximum common edge subgraph for multiple large networks.

	CytoMCS
	Computes the maximum common edge subgraph for multiple large networks.
	(8) 6956 downloads

	RINspector
	Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions

	RINspector
	Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions
	(5) 12777 downloads

	cyBrowser
	Core App: Add HTML Browser to Cytoscape

	cyBrowser
	Core App: Add HTML Browser to Cytoscape
	(1) 53207 downloads

	MetaNetter_2

	MetaNetter_2

	(1) 6614 downloads

	CytoCtrlAnalyser
	Integrated algorithms for the network control problem

	CytoCtrlAnalyser
	Integrated algorithms for the network control problem
	(4) 2988 downloads

	InformationAnalyzer

	InformationAnalyzer

	(14) 2368 downloads

	CyNDEx-2
	Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.

	CyNDEx-2
	Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
	(4) 70021 downloads

	TETRAMER
	A Temporal Transcription regulation modeler to predict master regulators

	TETRAMER
	A Temporal Transcription regulation modeler to predict master regulators
	(26) 3401 downloads

	InsituNet
	Analysis of in situ gene expression data in terms of spatial co-expression.

	InsituNet
	Analysis of in situ gene expression data in terms of spatial co-expression.
	(3) 8360 downloads

	yFiles Layout Algorithms
	Highly sophisticated algorithms for arranging networks.

	yFiles Layout Algorithms
	Highly sophisticated algorithms for arranging networks.
	(30) 254831 downloads

	Jesse
	Calculate the graphlet degrees of all nodes within a graph

	Jesse
	Calculate the graphlet degrees of all nodes within a graph
	(1) 4724 downloads

	CytoMOBAS
	Identifies and analyzes disease associated and highly connected subnetworks.

	CytoMOBAS
	Identifies and analyzes disease associated and highly connected subnetworks.
	(0) 4232 downloads

	autoHGPEC
	An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations

	autoHGPEC
	An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations
	(6) 8709 downloads

	DAPath
	Disease Associated Path Analyzer

	DAPath
	Disease Associated Path Analyzer
	(0) 5187 downloads

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints
	(2) 14045 downloads

	OmniPath
	OmniPath: literature curated human signaling pathways

	OmniPath
	OmniPath: literature curated human signaling pathways
	(17) 19178 downloads

	FlyScape
	MetScape metabolic network visualization for D. melanogaster

	FlyScape
	MetScape metabolic network visualization for D. melanogaster
	(1) 4475 downloads

	cyChart
	An interactive tool to define filters

	cyChart
	An interactive tool to define filters
	(1) 51283 downloads

	Highlighter
	Highlight and select nodes based on shared custom node annotations.

	Highlighter
	Highlight and select nodes based on shared custom node annotations.
	(1) 3741 downloads

	RWRMTN
	a tool for predicting disease-associated microRNAs based on a microRNA-target gene network

	RWRMTN
	a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
	(4) 3835 downloads

	Petri Net Implementation for Cytoscape
	Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets

	Petri Net Implementation for Cytoscape
	Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets
	(4) 3592 downloads

	scNetViz
	Single-cell RNASeq analysis in Cytoscape

	scNetViz
	Single-cell RNASeq analysis in Cytoscape
	(1) 18798 downloads

	UFO
	a tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization

	UFO
	a tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
	(2) 4737 downloads

	HDR
	Drug repositioning based on a heterogeneous network of drugs and diseases

	HDR
	Drug repositioning based on a heterogeneous network of drugs and diseases
	(1) 8061 downloads

	Assembly
	Import sequence graphs in Graphical Fragment Assembly (GFA) Format versions 1.0 and 2.0

	Assembly
	Import sequence graphs in Graphical Fragment Assembly (GFA) Format versions 1.0 and 2.0
	(2) 7635 downloads

	CyCommunityDetection
	Integrates multiscale community detection and functional enrichment for network analysis. CDAPS

	CyCommunityDetection
	Integrates multiscale community detection and functional enrichment for network analysis. CDAPS
	(1) 10875 downloads

	BNMatch2
	BNMatch provides a reliable and optimized mapping between networks considering about nodal information and topological similarity

	BNMatch2
	BNMatch provides a reliable and optimized mapping between networks considering about nodal information and topological similarity
	(3) 10192 downloads

	DKernel
	DKernel uses Diffusion Kernel algorithm to propagate sub-network for pathway analysis, disease vicinity, social network, etc.

	DKernel
	DKernel uses Diffusion Kernel algorithm to propagate sub-network for pathway analysis, disease vicinity, social network, etc.
	(1) 8365 downloads

	FileTransfer
	File system proxy for remote Jupyter Notebooks

	FileTransfer
	File system proxy for remote Jupyter Notebooks
	(1) 36984 downloads

	TimeNexus
	Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.

	TimeNexus
	Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
	(1) 2530 downloads

	Largest Subnetwork
	Selects the largest connected component in a network

	Largest Subnetwork
	Selects the largest connected component in a network
	(4) 11303 downloads

	PhageCocktail
	PhageCocktail App finds the best combination of phages lysing specified bacteria.

	PhageCocktail
	PhageCocktail App finds the best combination of phages lysing specified bacteria.
	(4) 2535 downloads

	NeDRex
	Finds drug repurposing candidates and disease modules. Builds custom heterogeneous molecular networks and allows for exploration

	NeDRex
	Finds drug repurposing candidates and disease modules. Builds custom heterogeneous molecular networks and allows for exploration
	(7) 9393 downloads

	Inbreeding
	Inbreeding app, given a mating network, calculates the inbreeding and relationship coefficients of all the individuals in the network.

	Inbreeding
	Inbreeding app, given a mating network, calculates the inbreeding and relationship coefficients of all the individuals in the network.
	(4) 2370 downloads

	EnrichmentTable
	Creates a new table for performing, storing and viewing functional enrichment analysis

	EnrichmentTable
	Creates a new table for performing, storing and viewing functional enrichment analysis
	(7) 21877 downloads

	WebbyMcSearch
	Perform web queries of a node attribute for selected node(s) on Google, PubMed, or other common search engines

	WebbyMcSearch
	Perform web queries of a node attribute for selected node(s) on Google, PubMed, or other common search engines
	(0) 2873 downloads

	CodeNetVis
	Explore the dependency graph of your software system interactively

	CodeNetVis
	Explore the dependency graph of your software system interactively
	(10) 2163 downloads

	DynDiffNet
	a Cytoscape app for dynamic differential network construction, analysis and visualization

	DynDiffNet
	a Cytoscape app for dynamic differential network construction, analysis and visualization
	(0) 1409 downloads

	CyEnGNet
	CyEnGNet: Cytoscape Ensemble Gene Network

	CyEnGNet
	CyEnGNet: Cytoscape Ensemble Gene Network
	(91) 2172 downloads

	MGG
	performs the microbetag workflow and visualise microbetag-annotated networks

	MGG
	performs the microbetag workflow and visualise microbetag-annotated networks
	(1) 2305 downloads

	ProteoVisualizer
	Functional analysis of MS-based proteomics data: from protein groups to networks

	ProteoVisualizer
	Functional analysis of MS-based proteomics data: from protein groups to networks
	(1) 2869 downloads

	CyArangoDB

	CyArangoDB

	(0) 631 downloads

	cymirCNV
	miRNA gene correlation network visualization

	cymirCNV
	miRNA gene correlation network visualization
	(1) 1165 downloads

	OpenCytoscapeWeb
	Open current network view on web.cytoscape.org in browser

	OpenCytoscapeWeb
	Open current network view on web.cytoscape.org in browser
	(0) 436 downloads

	Cytoscape MCP Server

	Cytoscape MCP Server

	(0) 156 downloads

Unsupported Plugins for Cytoscape 2.x

	MONET
	Predicts gene regulatory network from biological annotations and expression data.

	MONET
	Predicts gene regulatory network from biological annotations and expression data.
	(0)

	DomainGraph
	Visualizes domain-domain interactions which connect pairs of interacting proteins.

	DomainGraph
	Visualizes domain-domain interactions which connect pairs of interacting proteins.
	(7)

	CytoSQL
	Retrieves attributes from SQL databases by invoking query command.

	CytoSQL
	Retrieves attributes from SQL databases by invoking query command.
	(0)

	DroID
	Imports protein interaction networks from Drosophila Interactions Database (DroID).

	DroID
	Imports protein interaction networks from Drosophila Interactions Database (DroID).
	(3)

	MiMIplugin
	Retrieves molecular interactions and interaction attributes from MiMI and displays the interaction networks and attributes.

	MiMIplugin
	Retrieves molecular interactions and interaction attributes from MiMI and displays the interaction networks and attributes.
	(9)

	ConsensusPathDBplugin
	Retrieves interaction evidences for given pair of genes or proteins

	ConsensusPathDBplugin
	Retrieves interaction evidences for given pair of genes or proteins
	(4)

	bioCycPlugin
	Loads any pathway in bioCyc database. Original panel provides useful information for each node.

	bioCycPlugin
	Loads any pathway in bioCyc database. Original panel provides useful information for each node.
	(1)

	ReConn
	Loads pathway data from the reactome server and integrates expression data.

	ReConn
	Loads pathway data from the reactome server and integrates expression data.
	(0)

	Pathintegrator
	Pathintegrator searches for, and integrates in a single network pathways in which a given gene or protein is involved.

	Pathintegrator
	Pathintegrator searches for, and integrates in a single network pathways in which a given gene or protein is involved.
	(11)

	PhosphositePlus Web Service Client Module
	Integrates phosphorylation-related information into the network.

	PhosphositePlus Web Service Client Module
	Integrates phosphorylation-related information into the network.
	(2)

	SessionForWeb
	Saves Cytoscape session in Web format.

	SessionForWeb
	Saves Cytoscape session in Web format.
	(0)

	PICRClient

	PICRClient

	(0)

	FunNetViz
	Integrates and visualizes co-expression network and measures centrality.

	FunNetViz
	Integrates and visualizes co-expression network and measures centrality.
	(5)

	HyperEdgeEditor
	Enables one to create hyper-edge by Cytoscape editor.

	HyperEdgeEditor
	Enables one to create hyper-edge by Cytoscape editor.
	(0)

	PythonScriptingEngine
	Scripting language support for Python (Jython)

	PythonScriptingEngine
	Scripting language support for Python (Jython)
	(0)

	ScriptEngineManager
	Manager plugin required for all scripting engines

	ScriptEngineManager
	Manager plugin required for all scripting engines
	(1)

	CyGoose
	Provides Gaggle Boss, which routes data from one application to another.

	CyGoose
	Provides Gaggle Boss, which routes data from one application to another.
	(1)

	ClojureEngine
	Experimental support for Clojure scripts

	ClojureEngine
	Experimental support for Clojure scripts
	(0)

	IgraphPlugin
	Brings some functionality of Igraph such as layouts into Cytoscape. Mac only.

	IgraphPlugin
	Brings some functionality of Igraph such as layouts into Cytoscape. Mac only.
	(4)

	APCluster
	Uses affinity propagation described in Frey BJ and Duec D (2007) to perform clustering.

	APCluster
	Uses affinity propagation described in Frey BJ and Duec D (2007) to perform clustering.
	(5)

	MINE
	Clusters a network based on network topology using a modified agglomerative clustering algorithm very similar to MCODE.

	MINE
	Clusters a network based on network topology using a modified agglomerative clustering algorithm very similar to MCODE.
	(4)

	CyClus3D
	Clusters a network based on three-node motifs.

	CyClus3D
	Clusters a network based on three-node motifs.
	(1)

	GraphletCounter
	Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.

	GraphletCounter
	Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
	(1)

	RemainingDegreeDistribution
	Calculates remaining degree (excess degree) distribution.

	RemainingDegreeDistribution
	Calculates remaining degree (excess degree) distribution.
	(1)

	NetMatch
	Finds user defined network motifs in a given network. network motif can be created and edited using original GUI.

	NetMatch
	Finds user defined network motifs in a given network. network motif can be created and edited using original GUI.
	(2)

	ExprEssence
	Searches for differentially altered links in a given network using multiple set of expression data.

	ExprEssence
	Searches for differentially altered links in a given network using multiple set of expression data.
	(1)

	OmicsAnalyzer
	Integrates omics data such as expression data, proteome data, etc. onto networks

	OmicsAnalyzer
	Integrates omics data such as expression data, proteome data, etc. onto networks
	(3)

	PinnacleZ
	Identifies subnetworks which can discriminate given conditions according to PPI network and gene expression data

	PinnacleZ
	Identifies subnetworks which can discriminate given conditions according to PPI network and gene expression data
	(0)

	dynamicXpr
	Dynamically change colors of nodes like a movie according to their expression level across many conditions.

	dynamicXpr
	Dynamically change colors of nodes like a movie according to their expression level across many conditions.
	(2)

	SimTrek
	Assesses similarity of gene ontologies for given genes and their neighbours. All files must be installed in plugin folder.

	SimTrek
	Assesses similarity of gene ontologies for given genes and their neighbours. All files must be installed in plugin folder.
	(0)

	CABIN
	Integrates interaction datasets from various resources to explore and assess the resulting network

	CABIN
	Integrates interaction datasets from various resources to explore and assess the resulting network
	(0)

	OrthoNets
	Enables simultaneous comparison of interaction network of two species. protein domain information can be visualized.

	OrthoNets
	Enables simultaneous comparison of interaction network of two species. protein domain information can be visualized.
	(5)

	Reactome FIs
	Accesses to Reactome Functional interaction (FI) network to perform pathway analyses.

	Reactome FIs
	Accesses to Reactome Functional interaction (FI) network to perform pathway analyses.
	(4)

	structureViz
	Enables user to traverse from biological networks to detailed view of their structures.

	structureViz
	Enables user to traverse from biological networks to detailed view of their structures.
	(4)

	TransClust
	Clusters a given similarity graph.

	TransClust
	Clusters a given similarity graph.
	(12)

	APID2NET
	Downloads PPI data from APID and performs various analyses and visualizations.

	APID2NET
	Downloads PPI data from APID and performs various analyses and visualizations.
	(13)

	HiderSlider
	Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders.

	HiderSlider
	Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders.
	(0)

	CyOog

	CyOog

	(0)

	GroupTool
	Enables user to define groups of nodes and display information about groups.

	GroupTool
	Enables user to define groups of nodes and display information about groups.
	(0)

	edgeLengthPlugin
	Calculate edge length in the main network view window, and stores them as edge attributes "length".

	edgeLengthPlugin
	Calculate edge length in the main network view window, and stores them as edge attributes "length".
	(0)

	BiLayout
	Finds a bipartite network for two sets of user-selected nodes and performs layout.

	BiLayout
	Finds a bipartite network for two sets of user-selected nodes and performs layout.
	(8)

	GoogleChartFunctions
	Creates image from attribute values (URL) using the Google Chart API.

	GoogleChartFunctions
	Creates image from attribute values (URL) using the Google Chart API.
	(1)

	nodeCharts
	Paints bar, line or pie graphs onto nodes.

	nodeCharts
	Paints bar, line or pie graphs onto nodes.
	(2)

	PhyloTree
	Reads a file in phylogenetic tree format (Phylip or phyloXML) and visualizes it as a network.

	PhyloTree
	Reads a file in phylogenetic tree format (Phylip or phyloXML) and visualizes it as a network.
	(0)

	CytoSEED
	Enables users to view, manipulate and analyze metabolic models created by the Model SEED.

	CytoSEED
	Enables users to view, manipulate and analyze metabolic models created by the Model SEED.
	(3)

	Mosaic
	Systematically partition the given graph, and layout and color nodes based on GO terms.

	Mosaic
	Systematically partition the given graph, and layout and color nodes based on GO terms.
	(19)

	OWLPlugin
	Builds a network in Cytoscape from a user-provided OWL/RDF ontology and it implements a SPARQL module

	OWLPlugin
	Builds a network in Cytoscape from a user-provided OWL/RDF ontology and it implements a SPARQL module
	(0)

	SubnetworkCreator
	Create subnetworks for disconnected graphs.

	SubnetworkCreator
	Create subnetworks for disconnected graphs.
	(2)

	CARLSBAD
	Visualizes and explores chemical pattern bioactivity networks.

	CARLSBAD
	Visualizes and explores chemical pattern bioactivity networks.
	(1)

	MultiLevelLayout
	Layout algorithm for hierarchical biological networks.

	MultiLevelLayout
	Layout algorithm for hierarchical biological networks.
	(2)

	CySBML
	Cytoscape Plugin for SBML

	CySBML
	Cytoscape Plugin for SBML
	(7)

	ChartPlugin
	Create charts from numerical attributes of selected nodes or edges.

	ChartPlugin
	Create charts from numerical attributes of selected nodes or edges.
	(4)

	MultiColoredNodes
	Visualize several node attributes simultaneously using pie charts.

	MultiColoredNodes
	Visualize several node attributes simultaneously using pie charts.
	(11)

	NetTwo
	Measures functional relationship between two subnetworks

	NetTwo
	Measures functional relationship between two subnetworks
	(0)

	CyTableReaderPlugin
	A reader for CyTable attribute files

	CyTableReaderPlugin
	A reader for CyTable attribute files
	(0)

	NetDS
	Network Dynamics and Structure Analysis

	NetDS
	Network Dynamics and Structure Analysis
	(1)

	BiNoM
	Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.

	BiNoM
	Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
	(17)

	DvD

	DvD

	(6)

	BNMatch

	BNMatch

	(2)

	CytoHiCPlugin
	CytoHiC: Visual Comparison of Hi-C Networks

	CytoHiCPlugin
	CytoHiC: Visual Comparison of Hi-C Networks
	(0)

	NOA
	The Network Ontology Analysis plugin performs ontology overrepresentation analysis based on the network connections among annotate nodes.

	NOA
	The Network Ontology Analysis plugin performs ontology overrepresentation analysis based on the network connections among annotate nodes.
	(20)

	ContigScape
	An interactive guidance tool for microbial genome gap closure

	ContigScape
	An interactive guidance tool for microbial genome gap closure
	(2)

	SPNConverter
	Tool to convert graphs into GraphML format

	SPNConverter
	Tool to convert graphs into GraphML format
	(0)

	FNodeAtt

	FNodeAtt

	(0)

	MetaNetter
	Infers of metabolic networks based on high resolution metabolomic data.

	MetaNetter
	Infers of metabolic networks based on high resolution metabolomic data.
	(1)

	CyThesaurus-ID-Mapping
	Performs ID mapping using BridgeDb and other public or custom database sources.

	CyThesaurus-ID-Mapping
	Performs ID mapping using BridgeDb and other public or custom database sources.
	(10)

	BiogridPlugin
	Loads interaction data from the Biogrid database into Cytoscape

	BiogridPlugin
	Loads interaction data from the Biogrid database into Cytoscape
	(4)

	iRefScape
	Retrieves interactions associated with input IDs along with interaction details and iRefIndices.

	iRefScape
	Retrieves interactions associated with input IDs along with interaction details and iRefIndices.
	(0)

	PSICQUICUniversalClient
	PSICQUIC Web Service Client for importing interactions from public databases

	PSICQUICUniversalClient
	PSICQUIC Web Service Client for importing interactions from public databases
	(16)

	GraphMLReader
	Reader plugin for XML network files in GraphML format

	GraphMLReader
	Reader plugin for XML network files in GraphML format
	(0)

	KGMLReader
	File reader and pathway visualizer for KEGG XML (KGML) files

	KGMLReader
	File reader and pathway visualizer for KEGG XML (KGML) files
	(61)

	Superpathways-Plugin
	Downloads and integrates multiple pathways from Wikipathways.

	Superpathways-Plugin
	Downloads and integrates multiple pathways from Wikipathways.
	(0)

	GPML-Plugin
	Enables import of GPML file via import menu.

	GPML-Plugin
	Enables import of GPML file via import menu.
	(10)

	SFLDLoader
	Represents structural protein families and their homologs by graph on Cytoscape.

	SFLDLoader
	Represents structural protein families and their homologs by graph on Cytoscape.
	(0)

	Genoscape
	Visually integrates gene expression data sets from GenoScript and KEGG pathways into networks.

	Genoscape
	Visually integrates gene expression data sets from GenoScript and KEGG pathways into networks.
	(12)

	Commonattributes
	Find attributes shared between selected nodes.

	Commonattributes
	Find attributes shared between selected nodes.
	(0)

	FluxViz
	CyFluxViz - Visualize flux distributions

	FluxViz
	CyFluxViz - Visualize flux distributions
	(6)

	JavaScriptEngine
	Scripting support for JavaScript programming language

	JavaScriptEngine
	Scripting support for JavaScript programming language
	(0)

	RubyScriptingEngine
	Scripting support module for Ruby (JRuby) programming language

	RubyScriptingEngine
	Scripting support module for Ruby (JRuby) programming language
	(0)

	MiSink
	Provides network interface to MiSink-enabled Web sites, including DIP.

	MiSink
	Provides network interface to MiSink-enabled Web sites, including DIP.
	(0)

	CytoscapeRPC
	Allows user to query and modify networks through an XML-RPC connection.

	CytoscapeRPC
	Allows user to query and modify networks through an XML-RPC connection.
	(13)

	GroovyEngine
	Support for Groovy programming language

	GroovyEngine
	Support for Groovy programming language
	(0)

	Interference
	Evaluates the topological effects of node removal like Radiality, Closeness, Betweenness, Centroid Value and Eccentricity.

	Interference
	Evaluates the topological effects of node removal like Radiality, Closeness, Betweenness, Centroid Value and Eccentricity.
	(12)

	CommFinder
	Clustering based on QCUT, HQCUT, MCL, MCODE.

	CommFinder
	Clustering based on QCUT, HQCUT, MCL, MCODE.
	(5)

	NeMo
	Identifies densely connected and biopartite network modules.

	NeMo
	Identifies densely connected and biopartite network modules.
	(3)

	CalculatenodeDegree
	Simply calcuates degree for selected node.

	CalculatenodeDegree
	Simply calcuates degree for selected node.
	(0)

	Randomnetworks
	Generates random network or randomizes already loaded network.

	Randomnetworks
	Generates random network or randomizes already loaded network.
	(12)

	ShortestPath
	Finds shortest pathway between two selected nodes.

	ShortestPath
	Finds shortest pathway between two selected nodes.
	(3)

	BioQualiPlugin
	Performs consistency check of regulatory network and expression data.

	BioQualiPlugin
	Performs consistency check of regulatory network and expression data.
	(0)

	NetAtlas
	Integrates gene expression data of multiple tissues from Symatlas into network visualization and analysis.

	NetAtlas
	Integrates gene expression data of multiple tissues from Symatlas into network visualization and analysis.
	(2)

	PerturbationAnalyzer
	Evaluates how perturbation of selected nodes affect other nodes in a given network based on the law of mass action.

	PerturbationAnalyzer
	Evaluates how perturbation of selected nodes affect other nodes in a given network based on the law of mass action.
	(5)

	VistaClaraPlugin
	Provides effective visualization and analysis platform to analyse expression data on a given network.

	VistaClaraPlugin
	Provides effective visualization and analysis platform to analyse expression data on a given network.
	(5)

	clusterMaker
	Clusters densely connected nodes and node attributes in a given network.

	clusterMaker
	Clusters densely connected nodes and node attributes in a given network.
	(22)

	RDFScsape
	Allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.

	RDFScsape
	Allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.
	(13)

	NetworkEvolution
	Allows interactive comparative analysis of networks across different species.

	NetworkEvolution
	Allows interactive comparative analysis of networks across different species.
	(0)

	VennDiagramgenerator
	Generates a Venn/Euler Diagram of shared nodes for selected networks.

	VennDiagramgenerator
	Generates a Venn/Euler Diagram of shared nodes for selected networks.
	(0)

	ChemViz
	Visualizes chemical structure of each compound in chemical network with original interface.

	ChemViz
	Visualizes chemical structure of each compound in chemical network with original interface.
	(8)

	BLAST2similarityGraph
	Visualizes BLAST similarity as graph.

	BLAST2similarityGraph
	Visualizes BLAST similarity as graph.
	(11)

	clusterExplorerPlugin
	Explores a given similarity graph.

	clusterExplorerPlugin
	Explores a given similarity graph.
	(2)

	NetCirChro
	Visualizes interaction network on circular chromosomes.

	NetCirChro
	Visualizes interaction network on circular chromosomes.
	(4)

	ReOrientPlugin
	Layouts node positions according to reference Cytoscape session file.

	ReOrientPlugin
	Layouts node positions according to reference Cytoscape session file.
	(1)

	addParentNeighbors
	For a selected node in child network, adds neighboring nodes from a parent network .

	addParentNeighbors
	For a selected node in child network, adds neighboring nodes from a parent network .
	(0)

	MetanodePlugin2
	Enables user to define a group of nodes as a "meta node". Meta nodes can have hierarchy and can be expanded and collapsed.

	MetanodePlugin2
	Enables user to define a group of nodes as a "meta node". Meta nodes can have hierarchy and can be expanded and collapsed.
	(0)

	NamedSelection
	Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.

	NamedSelection
	Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.
	(0)

	FM3
	Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005.

	FM3
	Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005.
	(0)

	NeighborHighlight
	Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.

	NeighborHighlight
	Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
	(1)

	commandTool
	Provides simple command-line interface to Cytoscape.

	commandTool
	Provides simple command-line interface to Cytoscape.
	(0)

	FERN
	Performs stochastic simulation of chemical reaction networks.

	FERN
	Performs stochastic simulation of chemical reaction networks.
	(1)

	CytoSaddleSum
	Finds enriched function based on sum-of-weight scores.

	CytoSaddleSum
	Finds enriched function based on sum-of-weight scores.
	(0)

	CytoITMprobe
	Provides access to the ITM Probe database for querying and importing related network nodes and their attributes.

	CytoITMprobe
	Provides access to the ITM Probe database for querying and importing related network nodes and their attributes.
	(0)

	iCTNet
	Integrated Complex Traits Network (iCTNet) assembles human disease, tissue, gene and drug-target interactions.

	iCTNet
	Integrated Complex Traits Network (iCTNet) assembles human disease, tissue, gene and drug-target interactions.
	(6)

	KNIMEConnector
	Imports and exports networks from Konstanz Information Miner (KNIME)

	KNIMEConnector
	Imports and exports networks from Konstanz Information Miner (KNIME)
	(8)

	CytoSeVis
	Visualizes networks by semantic similarities.

	CytoSeVis
	Visualizes networks by semantic similarities.
	(0)

	NetLink
	Creates node or edge hyperlinks that open other networks.

	NetLink
	Creates node or edge hyperlinks that open other networks.
	(0)

	AlternativeTableImport
	Local data import through savable profiles

	AlternativeTableImport
	Local data import through savable profiles
	(2)

	IDSwitcher
	Change the identifier of your nodes or edges comfortably!

	IDSwitcher
	Change the identifier of your nodes or edges comfortably!
	(4)

	CytoKavosh
	Allows network motifs discovery

	CytoKavosh
	Allows network motifs discovery
	(4)

	NDBReaderPlugin
	A reader for Genomica NDB files

	NDBReaderPlugin
	A reader for Genomica NDB files
	(0)

	LayoutSaverPlugin

	LayoutSaverPlugin

	(0)

	GPEC
	Gene Prioritization and biomedical Evidence Collection

	GPEC
	Gene Prioritization and biomedical Evidence Collection
	(15)

	EnhancedSearch
	Performs searches on networks based on attributes

	EnhancedSearch
	Performs searches on networks based on attributes
	(3)

	HOMECAT
	Integrate data from multiple species, mapping multiple orthologs

	HOMECAT
	Integrate data from multiple species, mapping multiple orthologs
	(0)

	ModuLand
	Modularization method family offering modular hierarchies and adjustable overlaps

	ModuLand
	Modularization method family offering modular hierarchies and adjustable overlaps
	(10)

	MostHighlyConnectedSubgraphPlugin

	MostHighlyConnectedSubgraphPlugin

	(0)

	STOP
	Statistical Tracking of Ontological Phrases

	STOP
	Statistical Tracking of Ontological Phrases
	(4)

	ClustnSee
	Identification, visualization and analysis of clusters from large networks

	ClustnSee
	Identification, visualization and analysis of clusters from large networks
	(14)

	SimBoolNet
	SimBoolNet is a plugin for simulating the dynamics of signaling transduction using Boolean networks

	SimBoolNet
	SimBoolNet is a plugin for simulating the dynamics of signaling transduction using Boolean networks
	(2)

	IDARE [idare]
	Multiomics Visualisation and Network detangling

	IDARE [idare]
	Multiomics Visualisation and Network detangling
	(1)