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collections
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data visualization
(77)
network generation
(61)
network analysis
(60)
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(59)
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(47)
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(46)
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import
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interaction database
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scripting
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regulatory networks
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Random walk with restart algorithm
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network learning
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microarrays
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social network analysis
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shortest paths
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sequence similarity
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SBML
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R
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Pathway finding
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Gene prioritization
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gene co-expression
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structural biology
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JavaScript
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python
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protein dynamics
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post-translational modification
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pathway reconstruction
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network repository
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kegg
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inference
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Cancer
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bayesian networks
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ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(309) 314177 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.
(31) 180245 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) 177033 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 141481 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) 125186 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) 119529 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
(21) 101018 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) 82084 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) 73008 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) 66449 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) 57534 downloads
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 54199 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) 50451 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) 49589 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 42417 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) 39824 downloads
DisGeNET-app
The App is designed to visualize, query and analyse a network representation of DisGeNET data
DisGeNET-app
The App is designed to visualize, query and analyse a network representation of DisGeNET data
(9) 38139 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) 35087 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) 34397 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) 33384 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 30204 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) 28536 downloads
CyCL
Core App: Provides OpenCL support for Cytoscape
CyCL
Core App: Provides OpenCL support for Cytoscape
(0) 26692 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) 25514 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) 24200 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) 22904 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
(4) 21994 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17) 21014 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) 19852 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 19135 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) 19001 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) 18210 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 16865 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(3) 16170 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) 15460 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) 14630 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) 14585 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) 14089 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
(0) 13446 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(9) 13136 downloads
structureViz2
App to visualize macromolecular structures in a network context
structureViz2
App to visualize macromolecular structures in a network context
(4) 13016 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) 12566 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17) 12127 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 11814 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.
(6) 11626 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) 11519 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
(9) 11118 downloads
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
(12) 11035 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) 10835 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(6) 10730 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15) 10465 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 10155 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) 9774 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) 9365 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) 9346 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0) 9193 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 8971 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) 8817 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 8681 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(25) 8294 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
(0) 8073 downloads
WikiDataScape
A WikiData explorer for Cytoscape
WikiDataScape
A WikiData explorer for Cytoscape
(3) 7898 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) 7862 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) 7741 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5) 7603 downloads
CyGenexpi
Uncover regulatory interactions from time course data
CyGenexpi
Uncover regulatory interactions from time course data
(1) 7486 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) 7326 downloads
Color Cast
Applies a Brewer Color Palette to Network Nodes
Color Cast
Applies a Brewer Color Palette to Network Nodes
(7) 6920 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4) 6821 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) 6652 downloads
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(36) 6345 downloads
CyDataSeries
Add time series and the like to your networks.
CyDataSeries
Add time series and the like to your networks.
(1) 6310 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 6038 downloads
iCTNet2
iCTNet2
(1) 5955 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 5795 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) 5630 downloads
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7) 5187 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) 5171 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(14) 4966 downloads
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
(1) 4872 downloads
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
(8) 4804 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) 4745 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) 4533 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) 4467 downloads
TieDIE
Tied Diffusion Through Interacting Events
TieDIE
Tied Diffusion Through Interacting Events
(1) 4429 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) 4295 downloads
AnatApp
Elucidating functional networks of proteins
AnatApp
Elucidating functional networks of proteins
(1) 4225 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 4062 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) 3992 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) 3859 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) 3789 downloads
CyGraphSpace
Upload Cytoscape networks to GraphSpace
CyGraphSpace
Upload Cytoscape networks to GraphSpace
(3) 3670 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3614 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) 3371 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) 3336 downloads
SIREN
Signing of Regulatory Networks
SIREN
Signing of Regulatory Networks
(3) 3263 downloads
DAPath
Disease Associated Path Analyzer
DAPath
Disease Associated Path Analyzer
(0) 3136 downloads
CyFinder
CyFinder
(3) 3053 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 3015 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1) 2931 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) 2892 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) 2844 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) 2693 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) 2657 downloads
CytoAsp
CytoAsp
(0) 2568 downloads
ncINetView
ncINetView
(0) 2364 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) 2323 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 2281 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0) 2262 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3) 2179 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 2135 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1) 1981 downloads
Propagate
Propagate
(0) 1972 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 1881 downloads
MORO
MORO
(0) 1829 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) 1787 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 1768 downloads
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
(0) 1690 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2) 1596 downloads
EClerize
EClerize
(2) 1555 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) 1282 downloads
ZDOG
ZDOG
(0) 1195 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
(1) 869 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) 743 downloads
mapSourceAndTarget
mapSourceAndTarget
(2) 402 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) 225 downloads
ScyNet
Visualisation of community metabolic models
ScyNet
Visualisation of community metabolic models
(1) 117 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(30) 232729 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.
(76) 177652 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(27) 174403 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(25) 131102 downloads
cyREST
Core App: Language-agnostic RESTful API
cyREST
Core App: Language-agnostic RESTful API
(4) 122086 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.
(79) 115390 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(2) 85468 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 80012 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 70802 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) 62372 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) 54466 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) 53838 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) 50117 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 42513 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5) 40889 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 39799 downloads
Network Merge
Core App: Provides Cytoscape's Network Merge tool
Network Merge
Core App: Provides Cytoscape's Network Merge tool
(1) 37998 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 34852 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) 33943 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1) 30529 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) 28585 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 27394 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 26032 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
(2) 25070 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) 23576 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13) 22076 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 21466 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) 20829 downloads
chemViz2
Cheminformatics App for Cytoscape
chemViz2
Cheminformatics App for Cytoscape
(7) 19400 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) 19099 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.
(33) 18256 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) 17459 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) 16829 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) 15776 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) 14874 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 14609 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 14228 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) 13991 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) 13225 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) 13036 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 12958 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) 12279 downloads
D3.js Exporter
Network and Table Data Exporter for D3.js
D3.js Exporter
Network and Table Data Exporter for D3.js
(1) 12044 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) 11780 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2) 11619 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) 11132 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) 11047 downloads
CytoGEDEVO
Pairwise global alignment of PPI or other networks
CytoGEDEVO
Pairwise global alignment of PPI or other networks
(43) 10976 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) 10778 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) 10599 downloads
Welcome Screen
Core App: Provides Cytoscape welcome screen
Welcome Screen
Core App: Provides Cytoscape welcome screen
(0) 10406 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) 9777 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) 9605 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 9361 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) 9280 downloads
Cytoscape Neo4j Plugin
Cytoscape Neo4j Plugin
(5) 9022 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) 8901 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) 8681 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 8635 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) 8137 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) 8072 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) 7897 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1) 7770 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) 7643 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) 7580 downloads
NetMatchStar
An enhanced Cytoscape network querying app
NetMatchStar
An enhanced Cytoscape network querying app
(3) 7419 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 6920 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) 6858 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) 6657 downloads
GIANT
a Cytoscape plugin for network cartography
GIANT
a Cytoscape plugin for network cartography
(1) 6428 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2) 6332 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(57) 6229 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) 5975 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 5861 downloads
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
(5) 5692 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
(0) 5338 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) 5179 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) 4982 downloads
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
(31) 4931 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 4807 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).
(8) 4790 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 4737 downloads
Pesca3.0
Pesca3.0
(8) 4516 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1) 4445 downloads
bayelviraApp
Learning and generation of Bayesian networks.
bayelviraApp
Learning and generation of Bayesian networks.
(1) 4327 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 4273 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) 4209 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) 4000 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) 3931 downloads
MetaNetter_2
MetaNetter_2
(1) 3851 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 3715 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6) 3663 downloads
Diffany
Calculation of differential networks
Diffany
Calculation of differential networks
(4) 3439 downloads
Variation
Integrate variation and variation consequence data on biological networks.
Variation
Integrate variation and variation consequence data on biological networks.
(0) 3350 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) 3268 downloads
CycleDetector
Detects Cycles in a Cytoscape network
CycleDetector
Detects Cycles in a Cytoscape network
(0) 3208 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) 3076 downloads
FlyScape
MetScape metabolic network visualization for D. melanogaster
FlyScape
MetScape metabolic network visualization for D. melanogaster
(1) 3039 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0) 3008 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
(2) 2903 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) 2885 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) 2775 downloads
Cytoscape RedisGraph Plugin
Cytoscape RedisGraph Plugin
(1) 2680 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) 2633 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 2430 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(26) 2348 downloads
AOPXplorer
AOPXplorer
(0) 2309 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 2279 downloads
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
(4) 2205 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) 2164 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) 1994 downloads
CytoCtrlAnalyser
Integrated algorithms for the network control problem
CytoCtrlAnalyser
Integrated algorithms for the network control problem
(4) 1979 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) 1895 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) 1849 downloads
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
(3) 1821 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(25) 1768 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) 1738 downloads
InformationAnalyzer
InformationAnalyzer
(13) 1614 downloads
netIMP
Visualize IMP pathway models
netIMP
Visualize IMP pathway models
(0) 1560 downloads
cyTRON
cyTRON
(0) 1314 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.
(0) 1280 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) 1008 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) 829 downloads
CodeNetVis
Explore the dependency graph of your software system interactively
CodeNetVis
Explore the dependency graph of your software system interactively
(10) 470 downloads
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
(3) 295 downloads
ColorCodingApp
ColorCodingApp
(0) 171 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)
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)
SPNConverter
Tool to convert graphs into GraphML format
SPNConverter
Tool to convert graphs into GraphML format
(0)
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.
(0)
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)
DvD
DvD
(6)
BNMatch
BNMatch
(2)
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
(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)
FNodeAtt
FNodeAtt
(0)