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Categories
collections
(4)
data visualization
(78)
network generation
(61)
network analysis
(60)
graph analysis
(58)
online data import
(47)
automation
(44)
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(39)
clustering
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systems biology
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layout
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core app
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ontology analysis
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import
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network comparison
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gene expression
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local data import
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functional analysis
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PPI-network
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interaction database
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scripting
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Network structure
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network dynamics
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GO annotation
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regulatory networks
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Topology
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pathway
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network inference
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heat map visualization
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networks
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network manipulation
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export
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database
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cancer data analysis
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gene regulation
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functional module detection
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disease
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attribute generation
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animation
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network partitioning
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molecular structure
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linked data
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ID mapping
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grouping
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gene-disease association
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Connection sub-graph discovery
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simulation
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Random walk with restart algorithm
(6)
network learning
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microarrays
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centrality analysis
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social network analysis
(5)
shortest paths
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sequence similarity
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R
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Protein complex
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Pathway finding
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network alignment
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Gene prioritization
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gene co-expression
(5)
data manipulation
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cluster visualization
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3d visualization
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structural biology
(4)
SPARQL
(4)
signaling
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SBML
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literature mining
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kegg
(4)
JavaScript
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gene function prediction
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flux analysis
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variant analysis
(3)
set visualization
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set analysis
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search
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python
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protein dynamics
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pathway reconstruction
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network repository
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inference
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genome visualization
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disease-disease association
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Cancer
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Boolean Network
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bayesian networks
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Data visualization
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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) 3779 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2) 111 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 10886 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(23) 91374 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(0) 19753 downloads
CyDataSeries
Add time series and the like to your networks.
CyDataSeries
Add time series and the like to your networks.
(1) 4522 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2) 5005 downloads
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
(5) 4497 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) 14720 downloads
D3.js Exporter
Network and Table Data Exporter for D3.js
D3.js Exporter
Network and Table Data Exporter for D3.js
(1) 10053 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 19433 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) 9280 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.
(30) 14814 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) 2467 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) 3737 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) 17593 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.
(23) 41995 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(7) 7271 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
(3) 972 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 5110 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3021 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.
(1) 7271 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) 1399 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) 8693 downloads
SyncVis
Synchronous Visualizer
SyncVis
Synchronous Visualizer
(1) 1358 downloads
TieDIE
Tied Diffusion Through Interacting Events
TieDIE
Tied Diffusion Through Interacting Events
(1) 3481 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.
(34) 20992 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0) 7320 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(23) 106748 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 6449 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 9393 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(285) 235269 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 19517 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 11461 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 3391 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 3458 downloads
CytoKegg
Find Kegg pathways in a network. Import KEGG pathways into cytoscape.
CytoKegg
Find Kegg pathways in a network. Import KEGG pathways into cytoscape.
(61) 36737 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 14376 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 3624 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 10735 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 85092 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 4472 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 322 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(2) 64407 downloads
MetaNetter_2
MetaNetter_2
(0) 2406 downloads
MSClustering
provides an automated, efficient, and hierarchical clustering of complex networks without any parameter.
MSClustering
provides an automated, efficient, and hierarchical clustering of complex networks without any parameter.
(1) 226 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) 1986 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) 10417 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) 22173 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) 5870 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) 1185 downloads
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(35) 5582 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(22) 130361 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
(72) 29318 downloads
Variation
Integrate variation and variation consequence data on biological networks.
Variation
Integrate variation and variation consequence data on biological networks.
(0) 2755 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) 5941 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
(3) 2744 downloads
Unsupported Plugins for Cytoscape 2.x
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)
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
(4)
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)
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
(0)
FluxViz
CyFluxViz - Visualize flux distributions
FluxViz
CyFluxViz - Visualize flux distributions
(6)
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)
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)
nodeCharts
Paints bar, line or pie graphs onto nodes.
nodeCharts
Paints bar, line or pie graphs onto nodes.
(2)
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)
STOP
Statistical Tracking of Ontological Phrases
STOP
Statistical Tracking of Ontological Phrases
(4)
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)
ClustnSee
Identification, visualization and analysis of clusters from large networks
ClustnSee
Identification, visualization and analysis of clusters from large networks
(14)
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
(7)
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)
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
(0)
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
(61)
MultiColoredNodes
Visualize several node attributes simultaneously using pie charts.
MultiColoredNodes
Visualize several node attributes simultaneously using pie charts.
(11)
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)
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)
