Submit an App
Submit a 3.0 App
Guide to 3.0 App Development
Sign In
All Apps
Categories
collections
(4)
data visualization
(76)
network generation
(61)
network analysis
(60)
graph analysis
(59)
online data import
(47)
automation
(46)
integrated analysis
(38)
clustering
(38)
systems biology
(33)
utility
(32)
enrichment analysis
(31)
visualization
(29)
data integration
(28)
core app
(25)
layout
(22)
annotation
(21)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
interaction database
(15)
PPI-network
(14)
Network structure
(14)
scripting
(13)
network dynamics
(13)
GO annotation
(12)
regulatory networks
(11)
Topology
(10)
network inference
(10)
heat map visualization
(10)
pathway
(9)
networks
(9)
network manipulation
(9)
export
(9)
cancer data analysis
(9)
gene regulation
(8)
functional module detection
(8)
disease
(8)
database
(8)
attribute generation
(8)
animation
(8)
network partitioning
(7)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
grouping
(7)
gene-disease association
(7)
Connection sub-graph discovery
(7)
centrality analysis
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
3d visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
gene co-expression
(5)
data manipulation
(5)
cluster visualization
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
search
(4)
SBML
(4)
literature mining
(4)
JavaScript
(4)
gene function prediction
(4)
flux analysis
(4)
variant analysis
(3)
set visualization
(3)
set analysis
(3)
python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(3)
network repository
(3)
kegg
(3)
inference
(3)
genome visualization
(3)
disease-disease association
(3)
Cancer
(3)
Boolean Network
(3)
bayesian networks
(3)
Ontology analysis
Search for posts about ontology analysis →
Ask a question about ontology analysis →
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.
(76) 173823 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
(103) 171495 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) 33424 downloads
PiNGO
Finds candidate genes in a network that are associated with user-defined target GO terms.
PiNGO
Finds candidate genes in a network that are associated with user-defined target GO terms.
(4) 4278 downloads
WikiDataScape
A WikiData explorer for Cytoscape
WikiDataScape
A WikiData explorer for Cytoscape
(3) 7682 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(307) 303953 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) 120426 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
(55) 13739 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) 2659 downloads
WordCloud
Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
WordCloud
Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
(2) 55798 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)
Mosaic
Systematically partition the given graph, and layout and color nodes based on GO terms.
Mosaic
Systematically partition the given graph, and layout and color nodes based on GO terms.
(19)
OWLPlugin
Builds a network in Cytoscape from a user-provided OWL/RDF ontology and it implements a SPARQL module
OWLPlugin
Builds a network in Cytoscape from a user-provided OWL/RDF ontology and it implements a SPARQL module
(0)
SimTrek
Assesses similarity of gene ontologies for given genes and their neighbours. All files must be installed in plugin folder.
SimTrek
Assesses similarity of gene ontologies for given genes and their neighbours. All files must be installed in plugin folder.
(0)
CytoSeVis
Visualizes networks by semantic similarities.
CytoSeVis
Visualizes networks by semantic similarities.
(0)
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)
RDFScsape
Allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.
RDFScsape
Allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.
(13)
STOP
Statistical Tracking of Ontological Phrases
STOP
Statistical Tracking of Ontological Phrases
(4)