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collections
(4)
data visualization
(75)
network generation
(58)
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(55)
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(54)
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(46)
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(39)
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(34)
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(32)
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(31)
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(29)
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(28)
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(28)
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(21)
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(21)
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(20)
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(18)
pathway database
(17)
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import
(17)
gene expression
(16)
functional analysis
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(13)
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(13)
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(12)
GO annotation
(12)
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Network structure
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export
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attribute generation
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animation
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ID mapping
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simulation
(6)
Random walk with restart algorithm
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pathway
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network partitioning
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network learning
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molecular structure
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microarrays
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social network analysis
(5)
R
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Protein complex
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Pathway finding
(5)
literature mining
(5)
data manipulation
(5)
Connection sub-graph discovery
(5)
structural biology
(4)
SPARQL
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set analysis
(4)
sequence similarity
(4)
network alignment
(4)
JavaScript
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Gene prioritization
(4)
gene function prediction
(4)
gene co-expression
(4)
signaling
(3)
shortest paths
(3)
set visualization
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search
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SBML
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network repository
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kegg
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inference
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disease-disease association
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cluster visualization
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bayesian networks
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Integrated analysis
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Analyzer
Analyzer
(0) 486 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
(89) 86497 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(2) 9415 downloads
iCTNet2
iCTNet2
(1) 3330 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) 33205 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 3945 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(12) 75 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) 6660 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) 3990 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(3) 3074 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) 4347 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 232 downloads
TMM
Predict the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways
TMM
Predict the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways
(0) 2316 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) 21918 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 4746 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
(13) 20179 downloads
IDARE [idare]
Multiomics Visualisation and Network detangling
IDARE [idare]
Multiomics Visualisation and Network detangling
(0) 619 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) 12485 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) 13858 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) 1871 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
(40) 15136 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 7780 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 2351 downloads
RINspector
Combines centrality analyses with DynaMine flexibility predictions
RINspector
Combines centrality analyses with DynaMine flexibility predictions
(2) 2073 downloads
SyncVis
Synchronous Visualizer
SyncVis
Synchronous Visualizer
(0) 521 downloads
Unsupported Plugins for Cytoscape 2.x
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)
ClustnSee
Identification, visualization and analysis of clusters from large networks
ClustnSee
Identification, visualization and analysis of clusters from large networks
(14)
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)
GPEC
Gene Prioritization and biomedical Evidence Collection
GPEC
Gene Prioritization and biomedical Evidence Collection
(15)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
KNIMEConnector
Imports and exports networks from Konstanz Information Miner (KNIME)
(8)
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)
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)
BioQualiPlugin
Performs consistency check of regulatory network and expression data.
BioQualiPlugin
Performs consistency check of regulatory network and expression data.
(0)
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)
FluxViz
CyFluxViz - Visualize flux distributions
FluxViz
CyFluxViz - Visualize flux distributions
(6)
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)
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.
(1)
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)
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)
