All Apps

Categories
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)  12815 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2)  14254 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)  39923 downloads
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
(10)  12319 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)  5637 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)  6885 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0)  2686 downloads
BioGateway Cytoscape Plugin
An explorative network building plugin that works with the BioGateway triple store
BioGateway Cytoscape Plugin
An explorative network building plugin that works with the BioGateway triple store
(8)  9206 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)  10349 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)  80699 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2)  11945 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2)  3142 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0)  4852 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2)  17686 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(313)  363586 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(28)  157542 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1)  699 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)  11247 downloads
ColorCodingApp
ColorCodingApp
(0)  492 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6)  4144 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)  39955 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1)  11026 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1)  2364 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(3)  20008 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1)  9541 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5)  46460 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1)  46391 downloads
CyCL
Core App: Provides OpenCL support for Cytoscape
CyCL
Core App: Provides OpenCL support for Cytoscape
(0)  29540 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)  7795 downloads
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
(91)  1150 downloads
CyGenexpi
Uncover regulatory interactions from time course data
CyGenexpi
Uncover regulatory interactions from time course data
(1)  9145 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4)  5049 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2)  7446 downloads
cymirCNV
miRNA gene correlation network visualization
cymirCNV
miRNA gene correlation network visualization
(1)  475 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)  59552 downloads
CyNetSVM
A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines
CyNetSVM
A Cytoscape App for Cancer Biomarker Identification Using Network Constrained Support Vector Machines
(3)  3313 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)  21201 downloads
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
(3)  2308 downloads
cyREST
Core App: Language-agnostic RESTful API
cyREST
Core App: Language-agnostic RESTful API
(4)  137613 downloads
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
(5)  6547 downloads
CytoAsp
CytoAsp
(0)  2946 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29)  11218 downloads
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
(0)  404 downloads
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
(31)  5712 downloads
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
(8)  5749 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)  113607 downloads
Cytoscape RedisGraph Plugin
Cytoscape RedisGraph Plugin
(1)  3408 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3)  23482 downloads
D3.js Exporter
Network and Table Data Exporter for D3.js
D3.js Exporter
Network and Table Data Exporter for D3.js
(1)  13586 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1)  5342 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35)  32241 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)  5576 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)  681 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)  11052 downloads
EClerize
EClerize
(2)  1936 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)  150538 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)  16754 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)  38597 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)  12717 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0)  3807 downloads
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(9)  975 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)  12333 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)  17856 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1)  6928 downloads
GIANT
a Cytoscape plugin for network cartography
GIANT
a Cytoscape plugin for network cartography
(1)  6964 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)  15815 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)  5737 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1)  3096 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0)  2810 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)  1579 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)  6423 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12)  35640 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)  60787 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1)  3688 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)  15484 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(4)  99129 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4)  8690 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)  29514 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)  15269 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15)  11867 downloads
MetaNetter_2
MetaNetter_2
(1)  5103 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)  61830 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)  9662 downloads
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
(15)  12242 downloads
ncINetView
ncINetView
(0)  2775 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0)  2315 downloads
netIMP
Visualize IMP pathway models
netIMP
Visualize IMP pathway models
(0)  1925 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)  74602 downloads
Network Merge
Core App: Provides Cytoscape's Network Merge tool
Network Merge
Core App: Provides Cytoscape's Network Merge tool
(1)  42274 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)  3083 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(26)  2498 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(9)  18098 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)  27945 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)  3283 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)  3446 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)  9960 downloads
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
(4)  2632 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)  26969 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)  2610 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)  3406 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)  11972 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)  14554 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)  5386 downloads
Propagate
Propagate
(0)  2281 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)  19660 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)  9535 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(23)  119054 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1)  4050 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)  8988 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)  3105 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)  18246 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1)  12761 downloads
ScyNet
Visualisation of community metabolic models
ScyNet
Visualisation of community metabolic models
(1)  977 downloads
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(36)  6815 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3)  19725 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)  3293 downloads
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
(12)  13309 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34)  323602 downloads
structureViz2
App to visualize macromolecular structures in a network context
structureViz2
App to visualize macromolecular structures in a network context
(4)  14913 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(26)  2805 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)  49516 downloads
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
(1)  1832 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)  3674 downloads
Venn and Euler Diagrams
Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
Venn and Euler Diagrams
Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
(36)  26054 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)  1868 downloads
WikiDataScape
A WikiData explorer for Cytoscape
WikiDataScape
A WikiData explorer for Cytoscape
(3)  9395 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1)  2935 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0)  10634 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(30)  220165 downloads
ZDOG
ZDOG
(0)  1561 downloads

Unsupported Plugins for Cytoscape 2.x

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)
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)
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)
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)
BioQualiPlugin
Performs consistency check of regulatory network and expression data.
BioQualiPlugin
Performs consistency check of regulatory network and expression data.
(0)
BNMatch
BNMatch
(2)
CalculatenodeDegree
Simply calcuates degree for selected node.
CalculatenodeDegree
Simply calcuates degree for selected node.
(0)
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
(4)
ClojureEngine
Experimental support for Clojure scripts
ClojureEngine
Experimental support for Clojure scripts
(0)
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)
commandTool
Provides simple command-line interface to Cytoscape.
commandTool
Provides simple command-line interface to Cytoscape.
(0)
Commonattributes
Find attributes shared between selected nodes.
Commonattributes
Find attributes shared between selected nodes.
(0)
ContigScape
An interactive guidance tool for microbial genome gap closure
ContigScape
An interactive guidance tool for microbial genome gap closure
(2)
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)
CySBML
Cytoscape Plugin for SBML
CySBML
Cytoscape Plugin for SBML
(7)
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)
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)
CytoSaddleSum
Finds enriched function based on sum-of-weight scores.
CytoSaddleSum
Finds enriched function based on sum-of-weight scores.
(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)
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)
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)
EnhancedSearch
Performs searches on networks based on attributes
EnhancedSearch
Performs searches on networks based on attributes
(3)
FERN
Performs stochastic simulation of chemical reaction networks.
FERN
Performs stochastic simulation of chemical reaction networks.
(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)
FunNetViz
Integrates and visualizes co-expression network and measures centrality.
FunNetViz
Integrates and visualizes co-expression network and measures centrality.
(5)
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)
GPML-Plugin
Enables import of GPML file via import menu.
GPML-Plugin
Enables import of GPML file via import menu.
(10)
GraphMLReader
Reader plugin for XML network files in GraphML format
GraphMLReader
Reader plugin for XML network files in GraphML format
(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)
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
(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)
IDSwitcher
Change the identifier of your nodes or edges comfortably!
IDSwitcher
Change the identifier of your nodes or edges comfortably!
(4)
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)
JavaScriptEngine
Scripting support for JavaScript programming language
JavaScriptEngine
Scripting support for JavaScript programming language
(0)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
(8)
MetaNetter
Infers of metabolic networks based on high resolution metabolomic data.
MetaNetter
Infers of metabolic networks based on high resolution metabolomic data.
(1)
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)
MiSink
Provides network interface to MiSink-enabled Web sites, including DIP.
MiSink
Provides network interface to MiSink-enabled Web sites, including DIP.
(0)
MONET
Predicts gene regulatory network from biological annotations and expression data.
MONET
Predicts gene regulatory network from biological annotations and expression data.
(0)
MostHighlyConnectedSubgraphPlugin
MostHighlyConnectedSubgraphPlugin
(0)
MultiLevelLayout
Layout algorithm for hierarchical biological networks.
MultiLevelLayout
Layout algorithm for hierarchical biological networks.
(2)
NDBReaderPlugin
A reader for Genomica NDB files
NDBReaderPlugin
A reader for Genomica NDB files
(0)
NeMo
Identifies densely connected and biopartite network modules.
NeMo
Identifies densely connected and biopartite network modules.
(3)
NetCirChro
Visualizes interaction network on circular chromosomes.
NetCirChro
Visualizes interaction network on circular chromosomes.
(4)
NetLink
Creates node or edge hyperlinks that open other networks.
NetLink
Creates node or edge hyperlinks that open other networks.
(0)
NetTwo
Measures functional relationship between two subnetworks
NetTwo
Measures functional relationship between two subnetworks
(0)
NOA
The Network Ontology Analysis plugin performs ontology overrepresentation analysis based on the network connections among annotate nodes.
NOA
The Network Ontology Analysis plugin performs ontology overrepresentation analysis based on the network connections among annotate nodes.
(20)
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)
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)
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)
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)
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)
PythonScriptingEngine
Scripting language support for Python (Jython)
PythonScriptingEngine
Scripting language support for Python (Jython)
(0)
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)
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)
ReOrientPlugin
Layouts node positions according to reference Cytoscape session file.
ReOrientPlugin
Layouts node positions according to reference Cytoscape session file.
(1)
ScriptEngineManager
Manager plugin required for all scripting engines
ScriptEngineManager
Manager plugin required for all scripting engines
(1)
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)
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)
SPNConverter
Tool to convert graphs into GraphML format
SPNConverter
Tool to convert graphs into GraphML format
(0)
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)
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
(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)