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)  11815 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2)  12617 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)  35650 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)  11716 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)  4584 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)  6140 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0)  2422 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)  7201 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)  9372 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)  77950 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2)  10937 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2)  2094 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0)  4321 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2)  15796 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(311)  339491 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(26)  143867 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1)  271 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)  9170 downloads
ColorCodingApp
ColorCodingApp
(0)  290 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6)  3846 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)  37132 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1)  9543 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1)  2128 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(3)  17434 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1)  8399 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5)  43336 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1)  42723 downloads
CyCL
Core App: Provides OpenCL support for Cytoscape
CyCL
Core App: Provides OpenCL support for Cytoscape
(0)  27887 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)  6294 downloads
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
(4)  595 downloads
CyGenexpi
Uncover regulatory interactions from time course data
CyGenexpi
Uncover regulatory interactions from time course data
(1)  8047 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4)  4578 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2)  6706 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)  8640 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)  8077 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)  4005 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73)  36285 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1)  20200 downloads
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7)  5367 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40)  45012 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)  36149 downloads
CytoCtrlAnalyser
Integrated algorithms for the network control problem
CytoCtrlAnalyser
Integrated algorithms for the network control problem
(4)  2200 downloads
CytoGEDEVO
Pairwise global alignment of PPI or other networks
CytoGEDEVO
Pairwise global alignment of PPI or other networks
(43)  11640 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)  145808 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0)  3259 downloads
Cytoscape Neo4j Plugin
Cytoscape Neo4j Plugin
(5)  9987 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)  20440 downloads
cyTRON
cyTRON
(0)  1448 downloads
DAPath
Disease Associated Path Analyzer
DAPath
Disease Associated Path Analyzer
(0)  3434 downloads
Diffany
Calculation of differential networks
Diffany
Calculation of differential networks
(4)  3613 downloads
DisGeNET-app
Query, analyze, and visualize DISGENET data
DisGeNET-app
Query, analyze, and visualize DISGENET data
(9)  44064 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31)  15218 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)  12320 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13)  22932 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11)  147544 downloads
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
(3)  26724 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(6)  11325 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)  19328 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1)  32287 downloads
FlyScape
MetScape metabolic network visualization for D. melanogaster
FlyScape
MetScape metabolic network visualization for D. melanogaster
(1)  3332 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)  30575 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)  123241 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5)  7883 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)  14933 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(58)  6620 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)  1996 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)  3510 downloads
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
(1)  5094 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)  15505 downloads
InformationAnalyzer
InformationAnalyzer
(13)  1738 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)  9285 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)  9978 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)  19048 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)  7084 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7)  6085 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)  21635 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1)  4722 downloads
mapSourceAndTarget
mapSourceAndTarget
(2)  676 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(14)  5305 downloads
MCODE
Clusters a given network based on topology to find densely connected regions.
MCODE
Clusters a given network based on topology to find densely connected regions.
(32)  201718 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)  9288 downloads
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(0)  242 downloads
MORO
MORO
(1)  1968 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)  2644 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3)  3898 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)  4867 downloads
NetMatchStar
An enhanced Cytoscape network querying app
NetMatchStar
An enhanced Cytoscape network querying app
(3)  8058 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)  1681 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)  13012 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)  5535 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)  20997 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17)  13361 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)  16984 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)  14377 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14)  23093 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)  2866 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)  3229 downloads
Pesca3.0
Pesca3.0
(9)  4824 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)  3484 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)  1267 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17)  22567 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5)  13710 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)  4230 downloads
ProteoVisualizer
Functional analysis of MS-based proteomics data: from protein groups to networks
ProteoVisualizer
Functional analysis of MS-based proteomics data: from protein groups to networks
(0)  478 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)  7324 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4)  7458 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)  30286 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)  7697 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)  10567 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0)  6452 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)  4540 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)  10202 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)  2032 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(1)  2973 downloads
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
(0)  1812 downloads
SIREN
Signing of Regulatory Networks
SIREN
Signing of Regulatory Networks
(3)  3448 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)  12231 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(25)  8783 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1)  5053 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)  4694 downloads
TieDIE
Tied Diffusion Through Interacting Events
TieDIE
Tied Diffusion Through Interacting Events
(1)  4732 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)  8765 downloads
Variation
Integrate variation and variation consequence data on biological networks.
Variation
Integrate variation and variation consequence data on biological networks.
(0)  3485 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)  8444 downloads
Welcome Screen
Core App: Provides Cytoscape welcome screen
Welcome Screen
Core App: Provides Cytoscape welcome screen
(0)  11002 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11)  86427 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)  61638 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)  13343 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)  1965 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)