All Apps

Categories
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(311)  327444 downloads
MCODE
Clusters a given network based on topology to find densely connected regions.
MCODE
Clusters a given network based on topology to find densely connected regions.
(32)  190897 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)  184260 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11)  145108 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.
(168)  132472 downloads
cyREST
Core App: Language-agnostic RESTful API
cyREST
Core App: Language-agnostic RESTful API
(4)  126192 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
(22)  105623 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(3)  88414 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)  75818 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)  67403 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)  59868 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)  56049 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)  54311 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
(13)  51731 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1)  43768 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)  42065 downloads
DisGeNET-app
Query, analyze, and visualize DISGENET data
DisGeNET-app
Query, analyze, and visualize DISGENET data
(9)  41336 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)  36283 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)  35467 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)  34758 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1)  31601 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)  29731 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3)  27440 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)  26183 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.
(35)  24666 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)  24026 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13)  22630 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17)  21999 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)  20551 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3)  20069 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)  19517 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)  18724 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3)  17510 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)  16930 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)  16380 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2)  15336 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)  14895 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)  14642 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1)  14265 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)  13899 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)  13581 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5)  13448 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17)  12895 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)  12514 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0)  12223 downloads
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)  12055 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)  11912 downloads
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
(12)  11533 downloads
CytoGEDEVO
Pairwise global alignment of PPI or other networks
CytoGEDEVO
Pairwise global alignment of PPI or other networks
(43)  11418 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)  11139 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.
(12)  11033 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15)  10765 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)  10335 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)  9987 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29)  9785 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)  9725 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0)  9551 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)  9233 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1)  9196 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)  8967 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(25)  8601 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)  8469 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)  8361 downloads
WikiDataScape
A WikiData explorer for Cytoscape
WikiDataScape
A WikiData explorer for Cytoscape
(3)  8290 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)  8123 downloads
CyGenexpi
Uncover regulatory interactions from time course data
CyGenexpi
Uncover regulatory interactions from time course data
(1)  7877 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5)  7764 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4)  7343 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)  7187 downloads
Color Cast
Applies a Brewer Color Palette to Network Nodes
Color Cast
Applies a Brewer Color Palette to Network Nodes
(7)  7087 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
(6)  6786 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2)  6573 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(57)  6476 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0)  6296 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7)  5978 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)  5911 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)  5452 downloads
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7)  5296 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(14)  5163 downloads
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
(31)  5140 downloads
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
(1)  5015 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)  4911 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)  4722 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)  4639 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1)  4607 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)  4483 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4)  4460 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)  4371 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)  4248 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)  4122 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)  3959 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3)  3814 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1)  3710 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)  3524 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)  3432 downloads
SIREN
Signing of Regulatory Networks
SIREN
Signing of Regulatory Networks
(3)  3380 downloads
DAPath
Disease Associated Path Analyzer
DAPath
Disease Associated Path Analyzer
(0)  3319 downloads
FlyScape
MetScape metabolic network visualization for D. melanogaster
FlyScape
MetScape metabolic network visualization for D. melanogaster
(1)  3214 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)  3175 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1)  3119 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)  3010 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)  2969 downloads
Cytoscape RedisGraph Plugin
Cytoscape RedisGraph Plugin
(1)  2845 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)  2739 downloads
CytoAsp
CytoAsp
(0)  2662 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(1)  2565 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)  2483 downloads
ncINetView
ncINetView
(0)  2456 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0)  2372 downloads
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
(4)  2305 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3)  2275 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1)  2075 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)  2030 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)  1988 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2)  1947 downloads
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
(3)  1932 downloads
MORO
MORO
(1)  1915 downloads
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
(0)  1768 downloads
netIMP
Visualize IMP pathway models
netIMP
Visualize IMP pathway models
(0)  1643 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.
(2)  1575 downloads
cyTRON
cyTRON
(0)  1400 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)  1182 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)  1018 downloads
CodeNetVis
Explore the dependency graph of your software system interactively
CodeNetVis
Explore the dependency graph of your software system interactively
(10)  647 downloads
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
(3)  485 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)  332 downloads
ColorCodingApp
ColorCodingApp
(0)  254 downloads
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
(0)  106 downloads

Unsupported Plugins for Cytoscape 2.x

IDARE [idare]
Multiomics Visualisation and Network detangling
IDARE [idare]
Multiomics Visualisation and Network detangling
(1)
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)
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)
MostHighlyConnectedSubgraphPlugin
MostHighlyConnectedSubgraphPlugin
(0)
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)
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)
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)