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collections
(4)
data visualization
(76)
network generation
(61)
network analysis
(59)
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(59)
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(47)
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(45)
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(38)
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(38)
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(32)
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core app
(25)
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(21)
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ontology analysis
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import
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gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
interaction database
(15)
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(14)
Network structure
(14)
scripting
(13)
network dynamics
(12)
GO annotation
(12)
regulatory networks
(11)
Topology
(10)
network inference
(10)
heat map visualization
(10)
pathway
(9)
networks
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network manipulation
(9)
export
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cancer data analysis
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gene regulation
(8)
functional module detection
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disease
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database
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attribute generation
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animation
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network partitioning
(7)
molecular structure
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linked data
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ID mapping
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grouping
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gene-disease association
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Connection sub-graph discovery
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
centrality analysis
(6)
3d visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
R
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Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
gene co-expression
(5)
data manipulation
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cluster visualization
(5)
structural biology
(4)
SPARQL
(4)
signaling
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search
(4)
SBML
(4)
literature mining
(4)
JavaScript
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gene function prediction
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flux analysis
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variant analysis
(3)
set visualization
(3)
set analysis
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python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(3)
network repository
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kegg
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inference
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genome visualization
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disease-disease association
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Cancer
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Boolean Network
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bayesian networks
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Network generation
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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) 63377 downloads
bayelviraApp
Learning and generation of Bayesian networks.
bayelviraApp
Learning and generation of Bayesian networks.
(1) 4167 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) 64174 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.
(21) 33112 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 24030 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) 3694 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 33405 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 17631 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) 108278 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.
(24) 49717 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) 11340 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) 11861 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) 26761 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) 9053 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(26) 2185 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 73223 downloads
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
(9) 10459 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) 4346 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
(103) 162244 downloads
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
(8) 4437 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) 47061 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) 18000 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(39) 39202 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) 11217 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(11) 26474 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) 2002 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(8) 11002 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(21) 92510 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) 6835 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(28) 195602 downloads
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
(0) 1066 downloads
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
(3) 8276 downloads
Unsupported Plugins for Cytoscape 2.x
AlternativeTableImport
Local data import through savable profiles
AlternativeTableImport
Local data import through savable profiles
(2)
BLAST2similarityGraph
Visualizes BLAST similarity as graph.
BLAST2similarityGraph
Visualizes BLAST similarity as graph.
(11)
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
ConsensusPathDBplugin
Retrieves interaction evidences for given pair of genes or proteins
(3)
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)
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
DomainGraph
Visualizes domain-domain interactions which connect pairs of interacting proteins.
(7)
FunNetViz
Integrates and visualizes co-expression network and measures centrality.
FunNetViz
Integrates and visualizes co-expression network and measures centrality.
(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)
MetaNetter
Infers of metabolic networks based on high resolution metabolomic data.
MetaNetter
Infers of metabolic networks based on high resolution metabolomic data.
(1)
MONET
Predicts gene regulatory network from biological annotations and expression data.
MONET
Predicts gene regulatory network from biological annotations and expression data.
(0)
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)
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)
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
PSICQUICUniversalClient
PSICQUIC Web Service Client for importing interactions from public databases
(16)
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)
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)
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
Superpathways-Plugin
Downloads and integrates multiple pathways from Wikipathways.
(0)
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
BiogridPlugin
Loads interaction data from the Biogrid database into Cytoscape
(4)
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)
CySBML
Cytoscape Plugin for SBML
CySBML
Cytoscape Plugin for SBML
(7)
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)
DroID
Imports protein interaction networks from Drosophila Interactions Database (DroID).
DroID
Imports protein interaction networks from Drosophila Interactions Database (DroID).
(3)
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)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
(8)
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)
NetDS
Network Dynamics and Structure Analysis
NetDS
Network Dynamics and Structure Analysis
(1)
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)
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)
Randomnetworks
Generates random network or randomizes already loaded network.
Randomnetworks
Generates random network or randomizes already loaded network.
(12)
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)
STOP
Statistical Tracking of Ontological Phrases
STOP
Statistical Tracking of Ontological Phrases
(4)
