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collections
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data visualization
(76)
network generation
(61)
network analysis
(60)
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(59)
online data import
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automation
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clustering
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systems biology
(33)
utility
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enrichment analysis
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visualization
(29)
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(28)
core app
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layout
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annotation
(21)
pathway database
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ontology analysis
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import
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gene expression
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network comparison
(16)
local data import
(16)
functional analysis
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interaction database
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PPI-network
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Network structure
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scripting
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network dynamics
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GO annotation
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regulatory networks
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Topology
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network inference
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heat map visualization
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pathway
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networks
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export
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cancer data analysis
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gene regulation
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functional module detection
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disease
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database
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attribute generation
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animation
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network partitioning
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molecular structure
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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
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centrality analysis
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simulation
(6)
Random walk with restart algorithm
(6)
network learning
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microarrays
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3d visualization
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social network analysis
(5)
shortest paths
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sequence similarity
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R
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Protein complex
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Pathway finding
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network alignment
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Gene prioritization
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gene co-expression
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data manipulation
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cluster visualization
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structural biology
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SPARQL
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signaling
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search
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SBML
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JavaScript
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gene function prediction
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flux analysis
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variant analysis
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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 reconstruction
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network repository
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kegg
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inference
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genome visualization
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disease-disease association
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Cancer
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Boolean Network
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bayesian networks
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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) 50597 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 11413 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) 26936 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
(4) 19267 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) 8553 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) 18938 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 3491 downloads
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 5739 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) 2582 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) 16980 downloads
cy3sabiork
SABIO-RK webservice access
cy3sabiork
SABIO-RK webservice access
(1) 7356 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 2261 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) 12354 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 1782 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) 2684 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) 2082 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(28) 208121 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
(3) 8987 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)
