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All Apps
Categories
collections
(4)
data visualization
(75)
network generation
(59)
network analysis
(58)
graph analysis
(58)
online data import
(46)
automation
(43)
integrated analysis
(39)
clustering
(37)
systems biology
(32)
utility
(31)
enrichment analysis
(29)
visualization
(28)
data integration
(28)
layout
(21)
core app
(21)
annotation
(21)
ontology analysis
(18)
pathway database
(17)
network comparison
(17)
local data import
(17)
import
(17)
gene expression
(16)
functional analysis
(16)
scripting
(13)
interaction database
(13)
PPI-network
(12)
GO annotation
(12)
regulatory networks
(11)
Network structure
(11)
network dynamics
(11)
network inference
(10)
Topology
(9)
heat map visualization
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export
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disease
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network manipulation
(8)
gene regulation
(8)
functional module detection
(8)
database
(8)
cancer data analysis
(8)
attribute generation
(8)
animation
(8)
pathway
(7)
networks
(7)
linked data
(7)
ID mapping
(7)
gene-disease association
(7)
centrality analysis
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network partitioning
(6)
network learning
(6)
molecular structure
(6)
microarrays
(6)
grouping
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social network analysis
(5)
sequence similarity
(5)
R
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Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
literature mining
(5)
Gene prioritization
(5)
data manipulation
(5)
Connection sub-graph discovery
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
shortest paths
(4)
set analysis
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
gene co-expression
(4)
disease-disease association
(4)
cluster visualization
(4)
variant analysis
(3)
set visualization
(3)
search
(3)
SBML
(3)
network repository
(3)
inference
(3)
genome visualization
(3)
flux analysis
(3)
bayesian networks
(3)
3d visualization
(3)
Automation
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aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(1) 6447 downloads
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 25608 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) 13348 downloads
chemViz2
Cheminformatics App for Cytoscape
chemViz2
Cheminformatics App for Cytoscape
(6) 11452 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(22) 73094 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5) 25078 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 2837 downloads
Cyni Toolbox
Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
Cyni Toolbox
Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
(25) 14068 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(39) 26437 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 13938 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.
(24) 63894 downloads
eXamine
A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
eXamine
A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
(30) 12761 downloads
ID Mapper
A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.
ID Mapper
A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.
(1) 8939 downloads
MCODE
Clusters a given network based on topology to find densely connected regions.
MCODE
Clusters a given network based on topology to find densely connected regions.
(28) 79315 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(5) 3366 downloads
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
(1) 8431 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) 4984 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) 604 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 11518 downloads
structureViz2
App to visualize macromolecular structures in a network context
structureViz2
App to visualize macromolecular structures in a network context
(3) 8580 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 47467 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) 31527 downloads
Analyzer
Calculate network, node, and edge statistics for any connected network
Analyzer
Calculate network, node, and edge statistics for any connected network
(1) 3319 downloads
autoHGPEC
An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations
autoHGPEC
An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations
(6) 2321 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 7348 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(267) 186624 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 4803 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(0) 15466 downloads
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
(4) 18944 downloads
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7) 4230 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 5839 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 50226 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
(1) 12555 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.
(78) 82836 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(2) 51423 downloads
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
(11) 5827 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 12007 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
(21) 61600 downloads
RINspector
Combines centrality analyses with DynaMine flexibility predictions
RINspector
Combines centrality analyses with DynaMine flexibility predictions
(3) 2767 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 1248 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(20) 82972 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 2962 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 617 downloads
Unsupported Plugins for Cytoscape 2.x
