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Categories
data visualization
(78)
network analysis
(64)
network generation
(62)
graph analysis
(60)
automation
(48)
online data import
(47)
clustering
(39)
integrated analysis
(37)
systems biology
(33)
utility
(32)
enrichment analysis
(32)
visualization
(31)
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
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Network structure
(14)
scripting
(13)
regulatory networks
(13)
network dynamics
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GO annotation
(12)
Topology
(10)
network inference
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heat map visualization
(10)
export
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pathway
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networks
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network manipulation
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functional module detection
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disease
(9)
cancer data analysis
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network partitioning
(8)
gene regulation
(8)
database
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attribute generation
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animation
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molecular structure
(7)
linked data
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ID mapping
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grouping
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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
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R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
data manipulation
(5)
structural biology
(4)
SPARQL
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signaling
(4)
search
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literature mining
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kegg
(4)
JavaScript
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gene function prediction
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flux analysis
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bayesian networks
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variant analysis
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subnetwork extraction
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set visualization
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set analysis
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python
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protein dynamics
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post-translational modification
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pathway reconstruction
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Pathway analysis
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non-coding RNA
(3)
network repository
(3)
inference
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graph clustering
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genome visualization
(3)
drug repurposing
(3)
disease module
(3)
disease-disease association
(3)
Community detection
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Cancer
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Boolean Network
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Network analysis
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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) 12213 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) 63942 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1) 594 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(1) 2311 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
(14) 55967 downloads
cymirCNV
miRNA gene correlation network visualization
cymirCNV
miRNA gene correlation network visualization
(1) 378 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) 166311 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 3512 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 31528 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) 609 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) 10804 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) 20559 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) 32334 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) 16221 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) 5490 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) 20137 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) 14927 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15) 11667 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) 9540 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 4147 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) 13983 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) 22449 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) 3434 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) 3327 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17) 24541 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) 18939 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) 32679 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) 11511 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 3894 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 2817 downloads
ZDOG
ZDOG
(0) 1518 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) 6730 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 17197 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(1) 3270 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) 7463 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3) 2535 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) 3266 downloads
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
(8) 5622 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) 110265 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) 5294 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.
(7) 13072 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13) 24036 downloads
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(9) 801 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) 12122 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(59) 7171 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) 6214 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 6504 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(14) 5703 downloads
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(0) 599 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) 12067 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) 5937 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(26) 2385 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 25211 downloads
Pesca3.0
Pesca3.0
(9) 5119 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) 11644 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 14775 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(23) 116199 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3985 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) 3014 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(25) 9336 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) 16792 downloads
Unsupported Plugins for Cytoscape 2.x
ClustnSee
Identification, visualization and analysis of clusters from large networks
ClustnSee
Identification, visualization and analysis of clusters from large networks
(14)
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)
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
ModuLand
Modularization method family offering modular hierarchies and adjustable overlaps
(10)
