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data visualization
(78)
network analysis
(64)
network generation
(63)
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(59)
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integrated analysis
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Random walk with restart algorithm
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microarrays
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python
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protein dynamics
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non-coding RNA
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inference
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Cytoscape
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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) 73256 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 14363 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) 42330 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) 67287 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 7999 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(27) 3656 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) 10554 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) 15427 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 10614 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) 9041 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 18744 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) 234110 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 30227 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 4200 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) 23802 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) 25761 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) 3854 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) 32636 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 18200 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 4719 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) 12739 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) 14449 downloads
