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All Apps
Categories
data visualization
(78)
network analysis
(64)
network generation
(62)
graph analysis
(60)
automation
(48)
online data import
(47)
clustering
(39)
integrated analysis
(37)
systems biology
(33)
utility
(32)
enrichment analysis
(32)
visualization
(31)
data integration
(27)
core app
(25)
annotation
(24)
layout
(22)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
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network comparison
(16)
local data import
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functional analysis
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PPI-network
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interaction database
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Network structure
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scripting
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regulatory networks
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network dynamics
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GO annotation
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Topology
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network inference
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heat map visualization
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export
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pathway
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networks
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network manipulation
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functional module detection
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disease
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cancer data analysis
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network partitioning
(8)
gene regulation
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database
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attribute generation
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animation
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molecular structure
(7)
linked data
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ID mapping
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grouping
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gene-disease association
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Connection sub-graph discovery
(7)
centrality analysis
(7)
3d visualization
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
gene co-expression
(6)
cluster visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
SBML
(5)
R
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Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
data manipulation
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structural biology
(4)
SPARQL
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signaling
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search
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literature mining
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kegg
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JavaScript
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gene function prediction
(4)
flux analysis
(4)
bayesian networks
(4)
variant analysis
(3)
subnetwork extraction
(3)
set visualization
(3)
set analysis
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python
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protein dynamics
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post-translational modification
(3)
pathway reconstruction
(3)
Pathway analysis
(3)
non-coding RNA
(3)
network repository
(3)
inference
(3)
graph clustering
(3)
genome visualization
(3)
drug repurposing
(3)
disease module
(3)
disease-disease association
(3)
Community detection
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Cancer
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Boolean Network
(3)
Annotation
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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) 62463 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 12793 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1) 8685 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) 31364 downloads
Legend Creator
A way to add legends of discrete and continuous mappings to your graph
Legend Creator
A way to add legends of discrete and continuous mappings to your graph
(5) 27275 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) 9457 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 2106 downloads
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
(1) 3170 downloads
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
(4) 2849 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(33) 296373 downloads
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
(4) 14587 downloads
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
(20) 18447 downloads
ClustnSee 3
clustering, module exploration and annotation
ClustnSee 3
clustering, module exploration and annotation
(1) 405 downloads
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(7) 455 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 2817 downloads
Mass Spec Collection
Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.
Mass Spec Collection
Collection of apps to facilitate network analysis of mass spectrometry data. By installing this app, you will be installing a set of apps.
(3) 14279 downloads
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(0) 358 downloads
Omics Analysis Collection
Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.
Omics Analysis Collection
Collection of apps to facilitate network analysis of omic data. By installing this app, you will be installing a set of apps.
(1) 21581 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3855 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 6650 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) 3257 downloads
Unsupported Plugins for Cytoscape 2.x
CySBML
Cytoscape Plugin for SBML
CySBML
Cytoscape Plugin for SBML
(7)
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)
EnhancedSearch
Performs searches on networks based on attributes
EnhancedSearch
Performs searches on networks based on attributes
(3)
