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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) 13454 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) 72704 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) 67753 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) 6478 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) 25631 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) 73165 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) 213328 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) 169080 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) 3827 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) 9018 downloads

	CytoCopteR
	A Cytoscape plug-in for training logic models

	CytoCopteR
	A Cytoscape plug-in for training logic models
	(29) 14232 downloads

	DynNetwork
	Visualize dynamic networks in Cytoscape 3.0

	DynNetwork
	Visualize dynamic networks in Cytoscape 3.0
	(13) 27405 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) 6564 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) 15958 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) 23705 downloads

	SemScape
	Visualizes Semantic Data Landscapes

	SemScape
	Visualizes Semantic Data Landscapes
	(36) 7459 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) 43069 downloads

	WikiPathways
	WikiPathways web service client and GPML file format importer

	WikiPathways
	WikiPathways web service client and GPML file format importer
	(11) 109676 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) 42186 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) 32404 downloads

	GenomeSpace
	Enables communication with GenomeSpace

	GenomeSpace
	Enables communication with GenomeSpace
	(5) 9268 downloads

	iRegulon
	Detects master regulators and cis-regulatory interactions

	iRegulon
	Detects master regulators and cis-regulatory interactions
	(12) 39430 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) 25234 downloads

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data

	HyperModules
	Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
	(1) 6388 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) 14204 downloads

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

	KEGGscape
	File reader and pathway visualizer for KEGG XML (KGML) files
	(4) 111076 downloads

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape

	clusterMaker2
	Multi-algorithm clustering app for Cytoscape
	(28) 179352 downloads

	setsApp
	Save and manipulate sets of nodes and edges

	setsApp
	Save and manipulate sets of nodes and edges
	(3) 23100 downloads

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

	D3.js Exporter
	Network and Table Data Exporter for D3.js
	(1) 15624 downloads

	KDDN
	Knowledge-fused Differential Dependency Network

	KDDN
	Knowledge-fused Differential Dependency Network
	(7) 7939 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) 41735 downloads

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

	Synapse Client
	Access your data on Synapse.org from within Cyoscape
	(1) 6653 downloads

	structureViz2
	App to visualize macromolecular structures in a network context

	structureViz2
	App to visualize macromolecular structures in a network context
	(4) 17177 downloads

	Propagate

	Propagate

	(0) 2628 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) 4743 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) 9397 downloads

	cyREST
	Core App: Language-agnostic RESTful API

	cyREST
	Core App: Language-agnostic RESTful API
	(4) 160958 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) 5472 downloads

	EntOptLayout
	Relative entropy optimization based layout plugin

	EntOptLayout
	Relative entropy optimization based layout plugin
	(6) 14461 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) 10304 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) 10719 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) 22175 downloads

	CyAnimator
	Simple key-frame animation for Cytoscape

	CyAnimator
	Simple key-frame animation for Cytoscape
	(5) 51976 downloads

	CytoGEDEVO
	Pairwise global alignment of PPI or other networks

	CytoGEDEVO
	Pairwise global alignment of PPI or other networks
	(43) 15393 downloads

	cy3sbml
	cy3sbml visualizes SBML models (Systems Biology Markup Language)

	cy3sbml
	cy3sbml visualizes SBML models (Systems Biology Markup Language)
	(3) 41298 downloads

	Pesca3.0

	Pesca3.0

	(9) 6033 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) 15569 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) 14851 downloads

	dot-app
	Import/export of Graphviz files in Cytoscape

	dot-app
	Import/export of Graphviz files in Cytoscape
	(31) 20651 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) 7689 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) 10646 downloads

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

	Network Merge
	Core App: Provides Cytoscape's Network Merge tool
	(1) 46449 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) 30145 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) 20720 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) 10139 downloads

	cyTransFinder
	Signal Transduction Pathway Finder

	cyTransFinder
	Signal Transduction Pathway Finder
	(3) 29961 downloads

	Cy3D
	Simple 3D Network Renderer App

	Cy3D
	Simple 3D Network Renderer App
	(3) 24120 downloads

	layoutSaver
	Map node positions from one network to another

	layoutSaver
	Map node positions from one network to another
	(1) 5589 downloads

	SIREN
	Signing of Regulatory Networks

	SIREN
	Signing of Regulatory Networks
	(3) 4261 downloads

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

	Mclique
	Maximal Cliques in a given Cytoscape network, sorted by size
	(16) 13725 downloads

	CyIsomorphism
	All possible subgraph isomorphisms

	CyIsomorphism
	All possible subgraph isomorphisms
	(4) 6084 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) 11811 downloads

	NetMatchStar
	An enhanced Cytoscape network querying app

	NetMatchStar
	An enhanced Cytoscape network querying app
	(3) 11226 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) 15968 downloads

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

	AutoAnnotate
	Finds clusters and visually annotates them with labels and groups.
	(37) 78853 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) 11128 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) 63358 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) 37721 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) 18369 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) 30480 downloads

	SiGNetApp
	A Cytoscape App for producing network inference benchmarking data

	SiGNetApp
	A Cytoscape App for producing network inference benchmarking data
	(0) 2576 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) 4146 downloads

	CX Support
	Core App: CX JSON file reader and writer

	CX Support
	Core App: CX JSON file reader and writer
	(3) 99687 downloads

	CycleDetector
	Detects Cycles in a Cytoscape network

	CycleDetector
	Detects Cycles in a Cytoscape network
	(0) 4224 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) 14030 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) 14021 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) 4062 downloads

	WikiDataScape
	A WikiData explorer for Cytoscape

	WikiDataScape
	A WikiData explorer for Cytoscape
	(3) 11371 downloads

	CompleteGraph
	Creates a new fully connected Cytoscape network of given size

	CompleteGraph
	Creates a new fully connected Cytoscape network of given size
	(6) 4695 downloads

	GNC
	Gene Network Coherence with direct and indirect relationships

	GNC
	Gene Network Coherence with direct and indirect relationships
	(60) 8906 downloads

	CyFinder

	CyFinder

	(3) 5252 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) 3819 downloads

	CyDataSeries
	Add time series and the like to your networks.

	CyDataSeries
	Add time series and the like to your networks.
	(1) 9065 downloads

	Diffusion
	Expand node selection using network propagation algorithms

	Diffusion
	Expand node selection using network propagation algorithms
	(35) 40863 downloads

	CyGenexpi
	Uncover regulatory interactions from time course data

	CyGenexpi
	Uncover regulatory interactions from time course data
	(1) 11676 downloads

	FileWatcher
	An App to Link Networks with Excel Files

	FileWatcher
	An App to Link Networks with Excel Files
	(0) 4947 downloads

	EClerize

	EClerize

	(2) 2386 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) 4012 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) 20283 downloads

	AOPXplorer

	AOPXplorer

	(0) 3266 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) 14254 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) 4468 downloads

	CyLinkPredictor
	Link Predictor Based on Common Neighbors

	CyLinkPredictor
	Link Predictor Based on Common Neighbors
	(3) 3169 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) 5120 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) 6020 downloads

	copycatLayout
	Clone a network view layout by mapping node column values

	copycatLayout
	Clone a network view layout by mapping node column values
	(1) 14361 downloads

	Cytoscape Neo4j Plugin

	Cytoscape Neo4j Plugin

	(5) 14325 downloads

	MORO

	MORO

	(1) 2520 downloads

	CountTriplets
	Counts graph triplets and plots significance profiles

	CountTriplets
	Counts graph triplets and plots significance profiles
	(1) 2892 downloads

	CyGraphSpace
	Upload Cytoscape networks to GraphSpace

	CyGraphSpace
	Upload Cytoscape networks to GraphSpace
	(3) 5539 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) 4045 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) 3046 downloads

	cyTRON

	cyTRON

	(0) 2127 downloads

	Cytoscape RedisGraph Plugin

	Cytoscape RedisGraph Plugin

	(1) 4386 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) 35137 downloads

	Omics Visualizer
	Import & Visualize several data for the same node

	Omics Visualizer
	Import & Visualize several data for the same node
	(10) 23965 downloads

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

	wk-shell-decomposition
	Performs a weighted k-shell decomposition
	(1) 3918 downloads

	cyPlot
	A utility to display data plots

	cyPlot
	A utility to display data plots
	(1) 50392 downloads

	CyPathia
	Mechanistic models of pathways for omics data interpretation and analysis

	CyPathia
	Mechanistic models of pathways for omics data interpretation and analysis
	(3) 2765 downloads

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

	OCSANA+
	Optimal Control and Simulation of Signaling Networks from Network Analysis
	(27) 3613 downloads

	ZDOG

	ZDOG

	(0) 2168 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) 13307 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) 3282 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) 18093 downloads

	CONAN
	Analysis of atom interaction networks for structure ensembles of biomolecules

	CONAN
	Analysis of atom interaction networks for structure ensembles of biomolecules
	(1) 5172 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) 30117 downloads

	SenseNet
	Analysis of atom interaction networks for structure ensembles of biomolecules

	SenseNet
	Analysis of atom interaction networks for structure ensembles of biomolecules
	(1) 7129 downloads

	IDARE
	Data Visualisation for Multi-Omics data

	IDARE
	Data Visualisation for Multi-Omics data
	(0) 4143 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) 4924 downloads

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

	causalpath-cytoscape-app
	Visualize CausalPath (causalpath.org) results in Cytoscape
	(2) 4952 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) 5282 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) 3641 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) 2488 downloads

	mapSourceAndTarget

	mapSourceAndTarget

	(2) 2040 downloads

	ColorCodingApp

	ColorCodingApp

	(0) 832 downloads

	ScyNet
	Visualisation of community metabolic models

	ScyNet
	Visualisation of community metabolic models
	(1) 2052 downloads

	CytoDiVR
	Dive into your Cytoscape networks in Virtual Reality

	CytoDiVR
	Dive into your Cytoscape networks in Virtual Reality
	(0) 982 downloads

	ClustnSee 3
	clustering, module exploration and annotation

	ClustnSee 3
	clustering, module exploration and annotation
	(1) 1484 downloads

	FunCoup
	Import and analyze Cytoscape networks from FunCoup

	FunCoup
	Import and analyze Cytoscape networks from FunCoup
	(10) 2934 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) 433 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) 164 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) 144052 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) 83131 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) 203654 downloads

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

	ClueGO
	Creates and visualizes a functionally grouped network of terms/pathways
	(318) 404955 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) 25965 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) 81375 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) 67103 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) 75688 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) 28030 downloads

	CyTargetLinker
	Flexible network extension app

	CyTargetLinker
	Flexible network extension app
	(40) 52121 downloads

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

	CyPath2
	Pathway Commons (BioPAX L3 database) web service GUI client app
	(73) 43785 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) 232972 downloads

	Cyrface
	Bridging Cytoscape with R

	Cyrface
	Bridging Cytoscape with R
	(7) 6278 downloads

	SLiMScape
	A Protein Short Linear Motif Analysis Plugin for Cytoscape

	SLiMScape
	A Protein Short Linear Motif Analysis Plugin for Cytoscape
	(12) 15654 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) 20176 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) 23666 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) 134446 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) 16838 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) 141329 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) 45322 downloads

	GIANT
	a Cytoscape plugin for network cartography

	GIANT
	a Cytoscape plugin for network cartography
	(1) 7532 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) 10521 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) 11172 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) 65605 downloads

	enhancedGraphics
	A passthrough mapper for charts and gradients

	enhancedGraphics
	A passthrough mapper for charts and gradients
	(11) 168731 downloads

	bayelviraApp
	Learning and generation of Bayesian networks.

	bayelviraApp
	Learning and generation of Bayesian networks.
	(1) 5203 downloads

	chemViz2
	Cheminformatics App for Cytoscape

	chemViz2
	Cheminformatics App for Cytoscape
	(8) 32163 downloads

	Worm Plot
	Sequence self-similarity directed graph visualization.

	Worm Plot
	Sequence self-similarity directed graph visualization.
	(0) 12643 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) 21605 downloads

	Variation
	Integrate variation and variation consequence data on biological networks.

	Variation
	Integrate variation and variation consequence data on biological networks.
	(0) 4256 downloads

	CyLineUp
	Visualizes data in network small multiples

	CyLineUp
	Visualizes data in network small multiples
	(2) 8645 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) 4176 downloads

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database

	cddApp
	Integration between Cytoscape the the NCBI Conserved Domain Database
	(0) 16232 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) 28242 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) 13148 downloads

	PINBPA
	Protein-interaction-network-based Pathway Analysis

	PINBPA
	Protein-interaction-network-based Pathway Analysis
	(5) 18062 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) 16632 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) 49113 downloads

	CytoAsp

	CytoAsp

	(0) 3480 downloads

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

	RenoDoI
	A visual analytics approach for integrated data-knowledge networks.
	(1) 4701 downloads

	ncINetView

	ncINetView

	(0) 3306 downloads

	AnatApp
	Elucidating functional networks of proteins

	AnatApp
	Elucidating functional networks of proteins
	(1) 5209 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) 13686 downloads

	Strongest Path
	An application for protein-protein interaction analysis

	Strongest Path
	An application for protein-protein interaction analysis
	(25) 10762 downloads

	CySpanningTree
	Spanning tree computation and MST heuristic for Travelling Salesman Problem

	CySpanningTree
	Spanning tree computation and MST heuristic for Travelling Salesman Problem
	(5) 7606 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) 25692 downloads

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

	PTMOracle
	Co-visualisation and co-analysis of PTM and PPI data
	(4) 10520 downloads

	PhosphoPath
	Visualization and analysis of quantitative proteome and phosphoproteome datasets

	PhosphoPath
	Visualization and analysis of quantitative proteome and phosphoproteome datasets
	(17) 30021 downloads

	TieDIE
	Tied Diffusion Through Interacting Events

	TieDIE
	Tied Diffusion Through Interacting Events
	(1) 6414 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) 17134 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) 13368 downloads

	CyCL
	Core App: Provides OpenCL support for Cytoscape

	CyCL
	Core App: Provides OpenCL support for Cytoscape
	(0) 32081 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) 11308 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) 12187 downloads

	Welcome Screen
	Core App: Provides Cytoscape welcome screen

	Welcome Screen
	Core App: Provides Cytoscape welcome screen
	(0) 13974 downloads

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

	aMatReader
	App to read adjacency matrix (.mat, .adj) files
	(2) 17461 downloads

	cdtReader
	Read Cluster 3 output files into Cytoscape

	cdtReader
	Read Cluster 3 output files into Cytoscape
	(0) 5875 downloads

	stringApp
	Import and augment Cytoscape networks from STRING

	stringApp
	Import and augment Cytoscape networks from STRING
	(34) 390060 downloads

	PathLinker
	Reconstructs signaling pathways from protein interaction networks

	PathLinker
	Reconstructs signaling pathways from protein interaction networks
	(14) 32977 downloads

	Diffany
	Calculation of differential networks

	Diffany
	Calculation of differential networks
	(4) 4336 downloads

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

	NCMine
	Finds functional modules in gene networks by Near-Clique Mining
	(3) 4732 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) 15409 downloads

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

	MCDS
	Approximates the minimum connected dominating set (MCDS) of directed networks.
	(14) 6879 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) 26373 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) 14469 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) 5848 downloads

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

	gexf-app
	Imports Graph Exchange XML Format (GEXF) files
	(1) 7907 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) 18738 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) 4552 downloads

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

	DeDaL
	Data-driven layout (PCA...), network alignement, network morphing.
	(1) 6084 downloads

	cy3sabiork
	SABIO-RK webservice access

	cy3sabiork
	SABIO-RK webservice access
	(1) 12041 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) 3566 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) 17379 downloads

	CHAT
	Identify contextually relevant hubs in biological networks

	CHAT
	Identify contextually relevant hubs in biological networks
	(2) 22098 downloads

	BEL Navigator
	Explore OpenBEL knowledge networks within Cytoscape 3.

	BEL Navigator
	Explore OpenBEL knowledge networks within Cytoscape 3.
	(0) 3255 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) 2786 downloads

	DisGeNET-app
	Query, analyze, and visualize DISGENET data

	DisGeNET-app
	Query, analyze, and visualize DISGENET data
	(9) 76687 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) 15267 downloads

	NDB Reader
	Cytoscape app for reading Genomica NDB files

	NDB Reader
	Cytoscape app for reading Genomica NDB files
	(0) 2872 downloads

	netIMP
	Visualize IMP pathway models

	netIMP
	Visualize IMP pathway models
	(0) 2394 downloads

	Color Cast
	Applies a Brewer Color Palette to Network Nodes

	Color Cast
	Applies a Brewer Color Palette to Network Nodes
	(7) 8496 downloads

	SAFE
	Spatial Analysis for Functional Enrichment

	SAFE
	Spatial Analysis for Functional Enrichment
	(0) 8674 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) 13384 downloads

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

	CytoGTA
	Module (cluster) detection in PPI network based on gene expressions
	(31) 6738 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) 18098 downloads

	PCM
	Assemble Predicted Clusters For better Proteins Cluster Detection

	PCM
	Assemble Predicted Clusters For better Proteins Cluster Detection
	(4) 3061 downloads

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

	CytoMCS
	Computes the maximum common edge subgraph for multiple large networks.
	(8) 6873 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) 12606 downloads

	cyBrowser
	Core App: Add HTML Browser to Cytoscape

	cyBrowser
	Core App: Add HTML Browser to Cytoscape
	(1) 52886 downloads

	MetaNetter_2

	MetaNetter_2

	(1) 6515 downloads

	CytoCtrlAnalyser
	Integrated algorithms for the network control problem

	CytoCtrlAnalyser
	Integrated algorithms for the network control problem
	(4) 2961 downloads

	InformationAnalyzer

	InformationAnalyzer

	(14) 2338 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) 69596 downloads

	TETRAMER
	A Temporal Transcription regulation modeler to predict master regulators

	TETRAMER
	A Temporal Transcription regulation modeler to predict master regulators
	(26) 3367 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) 8251 downloads

	yFiles Layout Algorithms
	Highly sophisticated algorithms for arranging networks.

	yFiles Layout Algorithms
	Highly sophisticated algorithms for arranging networks.
	(30) 254504 downloads

	Jesse
	Calculate the graphlet degrees of all nodes within a graph

	Jesse
	Calculate the graphlet degrees of all nodes within a graph
	(1) 4665 downloads

	CytoMOBAS
	Identifies and analyzes disease associated and highly connected subnetworks.

	CytoMOBAS
	Identifies and analyzes disease associated and highly connected subnetworks.
	(0) 4192 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) 8597 downloads

	DAPath
	Disease Associated Path Analyzer

	DAPath
	Disease Associated Path Analyzer
	(0) 5125 downloads

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints

	boundaryLayout
	A Force-Directed Network Layout with Custom Boundary Constraints
	(2) 13970 downloads

	OmniPath
	OmniPath: literature curated human signaling pathways

	OmniPath
	OmniPath: literature curated human signaling pathways
	(17) 19013 downloads

	FlyScape
	MetScape metabolic network visualization for D. melanogaster

	FlyScape
	MetScape metabolic network visualization for D. melanogaster
	(1) 4407 downloads

	cyChart
	An interactive tool to define filters

	cyChart
	An interactive tool to define filters
	(1) 51101 downloads

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

	Highlighter
	Highlight and select nodes based on shared custom node annotations.
	(1) 3707 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) 3800 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) 3527 downloads

	scNetViz
	Single-cell RNASeq analysis in Cytoscape

	scNetViz
	Single-cell RNASeq analysis in Cytoscape
	(1) 18451 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) 4683 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) 7917 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) 7524 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) 10718 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) 10011 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) 8213 downloads

	FileTransfer
	File system proxy for remote Jupyter Notebooks

	FileTransfer
	File system proxy for remote Jupyter Notebooks
	(1) 36887 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) 2495 downloads

	Largest Subnetwork
	Selects the largest connected component in a network

	Largest Subnetwork
	Selects the largest connected component in a network
	(4) 11198 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) 2466 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) 9227 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) 2307 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) 21648 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) 2840 downloads

	CodeNetVis
	Explore the dependency graph of your software system interactively

	CodeNetVis
	Explore the dependency graph of your software system interactively
	(10) 2111 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) 1377 downloads

	CyEnGNet
	CyEnGNet: Cytoscape Ensemble Gene Network

	CyEnGNet
	CyEnGNet: Cytoscape Ensemble Gene Network
	(91) 2118 downloads

	MGG
	performs the microbetag workflow and visualise microbetag-annotated networks

	MGG
	performs the microbetag workflow and visualise microbetag-annotated networks
	(1) 2225 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) 2812 downloads

	CyArangoDB

	CyArangoDB

	(0) 597 downloads

	cymirCNV
	miRNA gene correlation network visualization

	cymirCNV
	miRNA gene correlation network visualization
	(1) 1122 downloads

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

	OpenCytoscapeWeb
	Open current network view on web.cytoscape.org in browser
	(0) 390 downloads

	Cytoscape MCP Server

	Cytoscape MCP Server

	(0) 113 downloads