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Categories
data visualization
(78)
network analysis
(63)
network generation
(61)
graph analysis
(60)
automation
(48)
online data import
(47)
clustering
(39)
integrated analysis
(37)
utility
(32)
systems biology
(32)
enrichment analysis
(32)
visualization
(30)
data integration
(27)
core app
(25)
annotation
(24)
layout
(22)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
PPI-network
(15)
interaction database
(15)
Network structure
(14)
scripting
(13)
network dynamics
(13)
regulatory networks
(12)
GO annotation
(12)
Topology
(10)
network inference
(10)
heat map visualization
(10)
export
(10)
pathway
(9)
networks
(9)
network manipulation
(9)
functional module detection
(9)
disease
(9)
cancer data analysis
(9)
network partitioning
(8)
gene regulation
(8)
database
(8)
attribute generation
(8)
animation
(8)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
grouping
(7)
gene-disease association
(7)
Connection sub-graph discovery
(7)
centrality analysis
(7)
3d visualization
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
gene co-expression
(6)
cluster visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
SBML
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
data manipulation
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
search
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
flux analysis
(4)
bayesian networks
(4)
variant analysis
(3)
subnetwork extraction
(3)
set visualization
(3)
set analysis
(3)
python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(3)
Pathway analysis
(3)
network repository
(3)
inference
(3)
graph clustering
(3)
genome visualization
(3)
drug repurposing
(3)
disease module
(3)
disease-disease association
(3)
Community detection
(3)
Cancer
(3)
Boolean Network
(3)
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) 11763 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2) 12572 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) 35505 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) 11636 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) 4557 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) 6114 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0) 2412 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) 7148 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) 9347 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) 77698 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 10905 downloads
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2) 2060 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 4309 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 15748 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(311) 337926 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(26) 142926 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1) 248 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) 9087 downloads
ColorCodingApp
ColorCodingApp
(0) 281 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6) 3834 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) 37038 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 9507 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1) 2118 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(3) 17382 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1) 8366 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5) 43188 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 42558 downloads
CyCL
Core App: Provides OpenCL support for Cytoscape
CyCL
Core App: Provides OpenCL support for Cytoscape
(0) 27817 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) 6247 downloads
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
CyEnGNet
CyEnGNet: Cytoscape Ensemble Gene Network
(4) 580 downloads
CyGenexpi
Uncover regulatory interactions from time course data
CyGenexpi
Uncover regulatory interactions from time course data
(1) 8013 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 4558 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2) 6686 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) 8620 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) 8043 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) 3998 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 36218 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 19401 downloads
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7) 5357 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 44837 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) 36047 downloads
CytoCtrlAnalyser
Integrated algorithms for the network control problem
CytoCtrlAnalyser
Integrated algorithms for the network control problem
(4) 2191 downloads
CytoGEDEVO
Pairwise global alignment of PPI or other networks
CytoGEDEVO
Pairwise global alignment of PPI or other networks
(43) 11610 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) 144049 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 3236 downloads
Cytoscape Neo4j Plugin
Cytoscape Neo4j Plugin
(5) 9927 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) 20385 downloads
cyTRON
cyTRON
(0) 1439 downloads
DAPath
Disease Associated Path Analyzer
DAPath
Disease Associated Path Analyzer
(0) 3419 downloads
Diffany
Calculation of differential networks
Diffany
Calculation of differential networks
(4) 3600 downloads
DisGeNET-app
Query, analyze, and visualize DISGENET data
DisGeNET-app
Query, analyze, and visualize DISGENET data
(9) 43678 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 15190 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) 12288 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13) 22892 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 147209 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) 26641 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(6) 11294 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) 19282 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1) 32166 downloads
FlyScape
MetScape metabolic network visualization for D. melanogaster
FlyScape
MetScape metabolic network visualization for D. melanogaster
(1) 3317 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) 30435 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) 122796 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5) 7869 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) 14896 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(58) 6594 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) 1981 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) 3498 downloads
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
HyperModules
Interaction Network Algorithm to Analyse Gene Mutations and Clinical Data
(1) 5083 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) 15437 downloads
InformationAnalyzer
InformationAnalyzer
(13) 1731 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) 9091 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) 9937 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) 19001 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) 7061 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 6070 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) 21594 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1) 4699 downloads
mapSourceAndTarget
mapSourceAndTarget
(2) 658 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(14) 5289 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) 200239 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) 9269 downloads
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(0) 230 downloads
MORO
MORO
(1) 1962 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) 2618 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 3884 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) 4812 downloads
NetMatchStar
An enhanced Cytoscape network querying app
NetMatchStar
An enhanced Cytoscape network querying app
(3) 8020 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) 1662 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) 12976 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) 5510 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) 20916 downloads
OmniPath
OmniPath: literature curated human signaling pathways
OmniPath
OmniPath: literature curated human signaling pathways
(17) 13306 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) 16974 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) 14344 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 22986 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) 2850 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) 3220 downloads
Pesca3.0
Pesca3.0
(9) 4801 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) 3475 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) 1253 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17) 22480 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 13666 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) 4217 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) 441 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) 7308 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 7428 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) 30212 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) 7645 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) 10534 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 6425 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) 4530 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) 10163 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) 2020 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 2922 downloads
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
SiGNetApp
A Cytoscape App for producing network inference benchmarking data
(0) 1806 downloads
SIREN
Signing of Regulatory Networks
SIREN
Signing of Regulatory Networks
(3) 3434 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) 12190 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(25) 8766 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 5035 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) 4686 downloads
TieDIE
Tied Diffusion Through Interacting Events
TieDIE
Tied Diffusion Through Interacting Events
(1) 4719 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) 8713 downloads
Variation
Integrate variation and variation consequence data on biological networks.
Variation
Integrate variation and variation consequence data on biological networks.
(0) 3475 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) 8401 downloads
Welcome Screen
Core App: Provides Cytoscape welcome screen
Welcome Screen
Core App: Provides Cytoscape welcome screen
(0) 10951 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 85853 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) 61398 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) 13216 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) 1953 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) 68287 downloads
AnatApp
Elucidating functional networks of proteins
AnatApp
Elucidating functional networks of proteins
(1) 4411 downloads
AOPXplorer
AOPXplorer
(0) 2515 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) 1244 downloads
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 59590 downloads
bayelviraApp
Learning and generation of Bayesian networks.
bayelviraApp
Learning and generation of Bayesian networks.
(1) 4467 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.
(77) 185832 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) 11558 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) 13794 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) 5453 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) 18058 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 12416 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) 57690 downloads
chemViz2
Cheminformatics App for Cytoscape
chemViz2
Cheminformatics App for Cytoscape
(7) 21700 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) 189846 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) 23871 downloads
CodeNetVis
Explore the dependency graph of your software system interactively
CodeNetVis
Explore the dependency graph of your software system interactively
(10) 713 downloads
Color Cast
Applies a Brewer Color Palette to Network Nodes
Color Cast
Applies a Brewer Color Palette to Network Nodes
(7) 7215 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) 8534 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 2661 downloads
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
(9) 5045 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) 3617 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 79017 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) 5215 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 28133 downloads
CyArangoDB
CyArangoDB
(0) 43 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 44527 downloads
CycleDetector
Detects Cycles in a Cytoscape network
CycleDetector
Detects Cycles in a Cytoscape network
(0) 3383 downloads
CyDataSeries
Add time series and the like to your networks.
CyDataSeries
Add time series and the like to your networks.
(1) 6650 downloads
CyFinder
CyFinder
(3) 3414 downloads
CyGraphSpace
Upload Cytoscape networks to GraphSpace
CyGraphSpace
Upload Cytoscape networks to GraphSpace
(3) 3951 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) 52744 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3) 2315 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) 54594 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) 3068 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) 19816 downloads
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
CyPathia
Mechanistic models of pathways for omics data interpretation and analysis
(3) 1988 downloads
cyREST
Core App: Language-agnostic RESTful API
cyREST
Core App: Language-agnostic RESTful API
(4) 128426 downloads
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
(5) 5997 downloads
CytoAsp
CytoAsp
(0) 2707 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 10003 downloads
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
CytoDiVR
Dive into your Cytoscape networks in Virtual Reality
(0) 128 downloads
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
CytoGTA
Module (cluster) detection in PPI network based on gene expressions
(31) 5211 downloads
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
(8) 5162 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) 96136 downloads
Cytoscape RedisGraph Plugin
Cytoscape RedisGraph Plugin
(1) 2929 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 20672 downloads
D3.js Exporter
Network and Table Data Exporter for D3.js
D3.js Exporter
Network and Table Data Exporter for D3.js
(1) 12594 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 4959 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 29246 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) 4388 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) 390 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) 9960 downloads
EClerize
EClerize
(2) 1683 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) 137011 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) 13272 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) 36092 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) 12235 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0) 3256 downloads
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(4) 112 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) 11312 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) 15824 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 6279 downloads
GIANT
a Cytoscape plugin for network cartography
GIANT
a Cytoscape plugin for network cartography
(1) 6659 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) 15239 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) 4701 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 2678 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 2194 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) 1077 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) 5608 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 32918 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) 57013 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1) 3191 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) 14078 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(4) 91161 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4) 7553 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) 25623 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) 13827 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15) 10977 downloads
MetaNetter_2
MetaNetter_2
(1) 4243 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) 57619 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) 9093 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) 11339 downloads
ncINetView
ncINetView
(0) 2507 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 2014 downloads
netIMP
Visualize IMP pathway models
netIMP
Visualize IMP pathway models
(0) 1683 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) 68957 downloads
Network Merge
Core App: Provides Cytoscape's Network Merge tool
Network Merge
Core App: Provides Cytoscape's Network Merge tool
(1) 39554 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) 2792 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(26) 1997 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(9) 15177 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) 26506 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) 3016 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) 3050 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) 9589 downloads
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
PCM
Assemble Predicted Clusters For better Proteins Cluster Detection
(4) 2367 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) 24715 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) 2119 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) 3072 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) 10544 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) 13242 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) 4849 downloads
Propagate
Propagate
(0) 2071 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) 16869 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) 8464 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(22) 108667 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3763 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) 7437 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) 2689 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) 16805 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 10388 downloads
ScyNet
Visualisation of community metabolic models
ScyNet
Visualisation of community metabolic models
(1) 445 downloads
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(36) 6519 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 17927 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) 2432 downloads
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
SLiMScape
A Protein Short Linear Motif Analysis Plugin for Cytoscape
(12) 11761 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(32) 272550 downloads
structureViz2
App to visualize macromolecular structures in a network context
structureViz2
App to visualize macromolecular structures in a network context
(4) 13709 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(26) 2510 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) 43193 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) 1498 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) 3068 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) 24968 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) 1096 downloads
WikiDataScape
A WikiData explorer for Cytoscape
WikiDataScape
A WikiData explorer for Cytoscape
(3) 8412 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 2378 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0) 9702 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(29) 196113 downloads
ZDOG
ZDOG
(0) 1326 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)
AlternativeTableImport
Local data import through savable profiles
AlternativeTableImport
Local data import through savable profiles
(2)
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)
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)
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
(4)
BLAST2similarityGraph
Visualizes BLAST similarity as graph.
BLAST2similarityGraph
Visualizes BLAST similarity as graph.
(11)
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)
CARLSBAD
Visualizes and explores chemical pattern bioactivity networks.
CARLSBAD
Visualizes and explores chemical pattern bioactivity networks.
(1)
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)
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)
CommFinder
Clustering based on QCUT, HQCUT, MCL, MCODE.
CommFinder
Clustering based on QCUT, HQCUT, MCL, MCODE.
(5)
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
(4)
CyClus3D
Clusters a network based on three-node motifs.
CyClus3D
Clusters a network based on three-node motifs.
(1)
CyOog
CyOog
(0)
CyTableReaderPlugin
A reader for CyTable attribute files
CyTableReaderPlugin
A reader for CyTable attribute files
(0)
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
CytoHiCPlugin
CytoHiC: Visual Comparison of Hi-C Networks
(0)
CytoKavosh
Allows network motifs discovery
CytoKavosh
Allows network motifs discovery
(4)
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)
CytoSeVis
Visualizes networks by semantic similarities.
CytoSeVis
Visualizes networks by semantic similarities.
(0)
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
(7)
DvD
DvD
(6)
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)
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)
FluxViz
CyFluxViz - Visualize flux distributions
FluxViz
CyFluxViz - Visualize flux distributions
(6)
FNodeAtt
FNodeAtt
(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)
GPEC
Gene Prioritization and biomedical Evidence Collection
GPEC
Gene Prioritization and biomedical Evidence Collection
(15)
GraphletCounter
Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
GraphletCounter
Calculates "graphlet" (small connected non-isomorphic subgraph) degree distribution.
(1)
GroovyEngine
Support for Groovy programming language
GroovyEngine
Support for Groovy programming language
(0)
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)
HyperEdgeEditor
Enables one to create hyper-edge by Cytoscape editor.
HyperEdgeEditor
Enables one to create hyper-edge by Cytoscape editor.
(0)
IDARE [idare]
Multiomics Visualisation and Network detangling
IDARE [idare]
Multiomics Visualisation and Network detangling
(1)
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)
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)
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
(61)
LayoutSaverPlugin
LayoutSaverPlugin
(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)
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)
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
(10)
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)
MultiColoredNodes
Visualize several node attributes simultaneously using pie charts.
MultiColoredNodes
Visualize several node attributes simultaneously using pie charts.
(11)
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)
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)
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)
NetDS
Network Dynamics and Structure Analysis
NetDS
Network Dynamics and Structure Analysis
(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)
NetworkEvolution
Allows interactive comparative analysis of networks across different species.
NetworkEvolution
Allows interactive comparative analysis of networks across different species.
(0)
nodeCharts
Paints bar, line or pie graphs onto nodes.
nodeCharts
Paints bar, line or pie graphs onto nodes.
(2)
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)
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)
PICRClient
PICRClient
(0)
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
(16)
Randomnetworks
Generates random network or randomizes already loaded network.
Randomnetworks
Generates random network or randomizes already loaded network.
(12)
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)
RemainingDegreeDistribution
Calculates remaining degree (excess degree) distribution.
RemainingDegreeDistribution
Calculates remaining degree (excess degree) distribution.
(1)
RubyScriptingEngine
Scripting support module for Ruby (JRuby) programming language
RubyScriptingEngine
Scripting support module for Ruby (JRuby) programming language
(0)
SessionForWeb
Saves Cytoscape session in Web format.
SessionForWeb
Saves Cytoscape session in Web format.
(0)
ShortestPath
Finds shortest pathway between two selected nodes.
ShortestPath
Finds shortest pathway between two selected nodes.
(3)
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)
STOP
Statistical Tracking of Ontological Phrases
STOP
Statistical Tracking of Ontological Phrases
(4)
SubnetworkCreator
Create subnetworks for disconnected graphs.
SubnetworkCreator
Create subnetworks for disconnected graphs.
(2)
TransClust
Clusters a given similarity graph.
TransClust
Clusters a given similarity graph.
(12)
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)