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collections
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data visualization
(76)
network generation
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network analysis
(59)
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(58)
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(47)
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microarrays
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grouping
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gene-disease association
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Connection sub-graph discovery
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centrality analysis
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social network analysis
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shortest paths
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sequence similarity
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R
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Protein complex
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Pathway finding
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network alignment
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Gene prioritization
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gene co-expression
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data manipulation
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SPARQL
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signaling
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literature mining
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kegg
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JavaScript
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gene function prediction
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cluster visualization
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variant analysis
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search
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python
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protein dynamics
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pathway reconstruction
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network repository
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inference
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genome visualization
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bayesian networks
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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
(8) 8412 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.
(39) 27478 downloads
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
CONAN
Analysis of atom interaction networks for structure ensembles of biomolecules
(0) 413 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
(0) 1392 downloads
CyLinkPredictor
Link Predictor Based on Common Neighbors
CyLinkPredictor
Link Predictor Based on Common Neighbors
(3) 1342 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.
(146) 39983 downloads
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
CytoMOBAS
Identifies and analyzes disease associated and highly connected subnetworks.
(0) 1731 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 17196 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) 8467 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(12) 18223 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.
(3) 19847 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
(52) 10603 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) 1609 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) 14771 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.
(2) 8916 downloads
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
Mclique
Maximal Cliques in a given Cytoscape network, sorted by size
(15) 7644 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.
(11) 6840 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
(4) 8347 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) 14109 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) 2155 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) 1941 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(16) 15096 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) 9552 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) 20228 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.
(1) 6528 downloads
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
SenseNet
Analysis of atom interaction networks for structure ensembles of biomolecules
(0) 126 downloads
SyncVis
Synchronous Visualizer
SyncVis
Synchronous Visualizer
(1) 1126 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
(2) 772 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) 3099 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 9594 downloads
CountTriplets
Counts graph triplets and plots significance profiles
CountTriplets
Counts graph triplets and plots significance profiles
(0) 1206 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
(12) 36971 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
(2) 1987 downloads
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
CytoMCS
Computes the maximum common edge subgraph for multiple large networks.
(8) 3080 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) 33246 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) 787 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) 6469 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.
(30) 13733 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
(12) 8355 downloads
GNC
Gene Network Coherence with direct and indirect relationships
GNC
Gene Network Coherence with direct and indirect relationships
(55) 3993 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) 3246 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 4658 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(13) 3421 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) 6679 downloads
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 2670 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(18) 499 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 13869 downloads
Pesca3.0
Pesca3.0
(6) 3457 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) 6235 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 9647 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) 69615 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 2824 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) 892 downloads
Strongest Path
An application for protein-protein interaction analysis
Strongest Path
An application for protein-protein interaction analysis
(22) 5539 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 886 downloads
ZDOG
ZDOG
(0) 432 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)
