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Guide to 3.0 App Development
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Cytoscape 2.x Plugins
Categories
data visualization
(78)
network analysis
(64)
network generation
(63)
graph analysis
(60)
automation
(49)
online data import
(47)
clustering
(39)
integrated analysis
(37)
systems biology
(33)
visualization
(32)
utility
(32)
enrichment analysis
(32)
data integration
(27)
core app
(25)
annotation
(24)
layout
(22)
pathway database
(19)
import
(19)
ontology analysis
(18)
gene expression
(18)
PPI-network
(16)
network comparison
(16)
local data import
(16)
interaction database
(16)
functional analysis
(16)
Network structure
(14)
scripting
(13)
regulatory networks
(13)
network dynamics
(13)
GO annotation
(12)
Topology
(10)
pathway
(10)
network inference
(10)
heat map visualization
(10)
export
(10)
networks
(9)
network manipulation
(9)
functional module detection
(9)
disease
(9)
database
(9)
cancer data analysis
(9)
network partitioning
(8)
gene regulation
(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)
gene co-expression
(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)
data manipulation
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
search
(4)
Pathway analysis
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
flux analysis
(4)
bayesian networks
(4)
variant analysis
(3)
subnetwork extraction
(3)
set visualization
(3)
set analysis
(3)
python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(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)
Cytoscape
(3)
Community detection
(3)
Cancer
(3)
Boolean Network
(3)
Utility
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CompleteGraph
Creates a new fully connected Cytoscape network of given size
CompleteGraph
Creates a new fully connected Cytoscape network of given size
(6)
5134 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1)
57519 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3)
35865 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1)
38823 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5)
9940 downloads
JGF App
Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.
JGF App
Import / Export OpenBEL Networks. JSON Graph Format Network App handles more restrictive BEL schema.
(1)
10949 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)
39311 downloads
Obfuscator
Replaces names of nodes in one or more networks with random names, while preserving correspondence across networks.
Obfuscator
Replaces names of nodes in one or more networks with random names, while preserving correspondence across networks.
(1)
8688 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3)
25933 downloads
Cy3 Performance Reporter
A diagnostics tool for collecting information about Cytoscape 3 performance. Requires Cy3 beta2-SNAPSHOT or later. Doesn't work with beta1.
Cy3 Performance Reporter
A diagnostics tool for collecting information about Cytoscape 3 performance. Requires Cy3 beta2-SNAPSHOT or later. Doesn't work with beta1.
(0)
7195 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4)
7122 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31)
23337 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0)
5884 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1)
4146 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4)
13470 downloads
NetworksInfo-writer
Writes information about all networks of control panel in a .csv file
NetworksInfo-writer
Writes information about all networks of control panel in a .csv file
(0)
3904 downloads
PathExplorer
Finds paths, filters them based on node and edge attributes and saves them.
PathExplorer
Finds paths, filters them based on node and edge attributes and saves them.
(41)
16724 downloads
Vital AI Graph Visualization
Use Vital AI software to connect to Databases, Servers, and Hadoop/Spark
Vital AI Graph Visualization
Use Vital AI software to connect to Databases, Servers, and Hadoop/Spark
(7)
13612 downloads
