Submit an App
Submit a 3.0 App
Guide to 3.0 App Development
Sign In
All Apps
Categories
collections
(4)
data visualization
(75)
network generation
(58)
network analysis
(56)
graph analysis
(56)
online data import
(45)
automation
(43)
integrated analysis
(39)
clustering
(35)
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)
PPI-network
(12)
interaction database
(12)
GO annotation
(12)
regulatory networks
(11)
Network structure
(11)
network dynamics
(11)
network inference
(10)
Topology
(9)
heat map visualization
(9)
export
(9)
network manipulation
(8)
gene regulation
(8)
functional module detection
(8)
disease
(8)
cancer data analysis
(8)
attribute generation
(8)
animation
(8)
networks
(7)
linked data
(7)
ID mapping
(7)
gene-disease association
(7)
database
(7)
centrality analysis
(7)
simulation
(6)
Random walk with restart algorithm
(6)
pathway
(6)
network partitioning
(6)
network learning
(6)
molecular structure
(6)
microarrays
(6)
grouping
(6)
social network analysis
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
literature mining
(5)
Gene prioritization
(5)
data manipulation
(5)
Connection sub-graph discovery
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
set analysis
(4)
sequence similarity
(4)
network alignment
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
gene co-expression
(4)
disease-disease association
(4)
variant analysis
(3)
shortest paths
(3)
set visualization
(3)
search
(3)
SBML
(3)
network repository
(3)
inference
(3)
genome visualization
(3)
cluster visualization
(3)
bayesian networks
(3)
Import
Search for posts about import →
Ask a question about import →
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) 6815 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0) 1309 downloads
CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6) 1995 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 14671 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) 7191 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 3332 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) 2459 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(5) 2411 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(19) 73449 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(1) 5804 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 2071 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 17996 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(30) 7685 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) 9132 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) 8139 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 921 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) 932 downloads
Unsupported Plugins for Cytoscape 2.x
