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data visualization
(78)
network analysis
(64)
network generation
(63)
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(59)
online data import
(47)
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integrated analysis
(37)
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(33)
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Random walk with restart algorithm
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network learning
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microarrays
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gene co-expression
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set visualization
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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
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network repository
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inference
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genome visualization
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disease-disease association
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Cytoscape
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Cancer
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Integrated analysis
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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) 73186 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 14262 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) 42208 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) 67150 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 7956 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(27) 3625 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) 10529 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) 15307 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 10544 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) 9024 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 18509 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) 233206 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 30030 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 4155 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) 23700 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) 25667 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) 3835 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) 32441 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 18102 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 4708 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) 12635 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) 14311 downloads
