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Categories
data visualization
(78)
network analysis
(64)
network generation
(62)
graph analysis
(60)
automation
(48)
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(47)
clustering
(39)
integrated analysis
(37)
systems biology
(33)
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(32)
enrichment analysis
(32)
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(31)
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(27)
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(25)
annotation
(24)
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(22)
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(18)
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(18)
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gene expression
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(15)
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export
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Random walk with restart algorithm
(6)
network learning
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microarrays
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gene co-expression
(6)
cluster visualization
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shortest paths
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R
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JavaScript
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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 analysis
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non-coding RNA
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network repository
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inference
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graph clustering
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genome visualization
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drug repurposing
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disease module
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disease-disease association
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Community detection
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Cancer
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Enrichment analysis
Search for posts about enrichment analysis →
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AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 63197 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(313) 351072 downloads
ClusterViz
Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
ClusterViz
Clustering based on FAG-EC, EAGLE or MCODE. Found cluster can be subjected to GO enrichment analysis.
(13) 24333 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 21733 downloads
EnrichmentMap
Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
EnrichmentMap
Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
(29) 143931 downloads
EnrichmentTable
Creates a new table for performing, storing and viewing functional enrichment analysis
EnrichmentTable
Creates a new table for performing, storing and viewing functional enrichment analysis
(7) 15165 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) 31556 downloads
GOlorize
Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.
GOlorize
Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.
(2) 15541 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) 19548 downloads
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
(25) 59672 downloads
PINBPA
Protein-interaction-network-based Pathway Analysis
PINBPA
Protein-interaction-network-based Pathway Analysis
(5) 14166 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 6694 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 301354 downloads
UFO
a tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
UFO
a tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
(2) 3321 downloads
BiNGO
Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.
BiNGO
Calculates overrepresented GO terms in the network and display them as a network of significant GO terms.
(77) 190097 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) 197169 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1) 439 downloads
DAPath
Disease Associated Path Analyzer
DAPath
Disease Associated Path Analyzer
(0) 3631 downloads
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
(3) 27530 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) 37132 downloads
GeneMANIA
Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
GeneMANIA
Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
(79) 126894 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 34397 downloads
MetDisease
Annotates metabolic networks with MeSH disease terms and links to references.
MetDisease
Annotates metabolic networks with MeSH disease terms and links to references.
(5) 9505 downloads
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(0) 392 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) 113267 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 11271 downloads
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
(73) 45487 downloads
Unsupported Plugins for Cytoscape 2.x
CytoSaddleSum
Finds enriched function based on sum-of-weight scores.
CytoSaddleSum
Finds enriched function based on sum-of-weight scores.
(0)
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
HOMECAT
Integrate data from multiple species, mapping multiple orthologs
(0)
STOP
Statistical Tracking of Ontological Phrases
STOP
Statistical Tracking of Ontological Phrases
(4)
DvD
DvD
(6)
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)
