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All Apps
Categories
data visualization
(78)
network analysis
(62)
network generation
(61)
graph analysis
(60)
online data import
(47)
automation
(47)
clustering
(39)
integrated analysis
(37)
utility
(32)
systems biology
(32)
enrichment analysis
(32)
visualization
(29)
data integration
(27)
core app
(25)
annotation
(23)
layout
(22)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
PPI-network
(15)
interaction database
(15)
Network structure
(14)
scripting
(13)
network dynamics
(13)
GO annotation
(12)
regulatory networks
(11)
Topology
(10)
network inference
(10)
heat map visualization
(10)
export
(10)
pathway
(9)
networks
(9)
network manipulation
(9)
functional module detection
(9)
cancer data analysis
(9)
network partitioning
(8)
gene regulation
(8)
disease
(8)
database
(8)
attribute generation
(8)
animation
(8)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
grouping
(7)
gene-disease association
(7)
Connection sub-graph discovery
(7)
centrality analysis
(7)
3d visualization
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
cluster visualization
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
SBML
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
gene co-expression
(5)
data manipulation
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
search
(4)
literature mining
(4)
kegg
(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)
Pathway analysis
(3)
network repository
(3)
inference
(3)
graph clustering
(3)
genome visualization
(3)
disease-disease association
(3)
Community detection
(3)
Cancer
(3)
Boolean Network
(3)
bayesian networks
(3)
Import
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Adj Exporter
Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks
Adj Exporter
Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks
(12) 11568 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0) 2380 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6) 3778 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 27536 downloads
DyNet
Compare two or more networks and identify the most 'rewired' nodes.
DyNet
Compare two or more networks and identify the most 'rewired' nodes.
(6) 12068 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 6123 downloads
InsituNet
Analysis of in situ gene expression data in terms of spatial co-expression.
InsituNet
Analysis of in situ gene expression data in terms of spatial co-expression.
(3) 5469 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(9) 14435 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(31) 255455 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2) 12265 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 4256 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 74717 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 14951 downloads
General SPARQL
Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF
General SPARQL
Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF
(10) 15594 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) 15233 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 1977 downloads
SDP Model Builder
Cytoscape 3 app that interfaces with Selventa Development Platform
SDP Model Builder
Cytoscape 3 app that interfaces with Selventa Development Platform
(0) 1997 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) 12716 downloads
Unsupported Plugins for Cytoscape 2.x
