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Categories
data visualization
(78)
network analysis
(63)
network generation
(61)
graph analysis
(60)
automation
(48)
online data import
(47)
clustering
(39)
integrated analysis
(37)
utility
(32)
systems biology
(32)
enrichment analysis
(32)
visualization
(30)
data integration
(27)
core app
(25)
annotation
(24)
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)
regulatory networks
(12)
GO annotation
(12)
Topology
(10)
network inference
(10)
heat map visualization
(10)
export
(10)
pathway
(9)
networks
(9)
network manipulation
(9)
functional module detection
(9)
disease
(9)
cancer data analysis
(9)
network partitioning
(8)
gene regulation
(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)
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)
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)
Pathway analysis
(3)
network repository
(3)
inference
(3)
graph clustering
(3)
genome visualization
(3)
drug repurposing
(3)
disease module
(3)
disease-disease association
(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) 3846 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 42723 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 20740 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1) 32287 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5) 7883 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) 7084 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) 25872 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) 5535 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 18000 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) 5224 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 4578 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 15218 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0) 3274 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 2695 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4) 7589 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) 2801 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) 14377 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) 8444 downloads
Unsupported Plugins for Cytoscape 2.x
AlternativeTableImport
Local data import through savable profiles
AlternativeTableImport
Local data import through savable profiles
(2)
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
ChartPlugin
Create charts from numerical attributes of selected nodes or edges.
(4)
CyTableReaderPlugin
A reader for CyTable attribute files
CyTableReaderPlugin
A reader for CyTable attribute files
(0)
GroupTool
Enables user to define groups of nodes and display information about groups.
GroupTool
Enables user to define groups of nodes and display information about groups.
(0)
IDSwitcher
Change the identifier of your nodes or edges comfortably!
IDSwitcher
Change the identifier of your nodes or edges comfortably!
(4)
NDBReaderPlugin
A reader for Genomica NDB files
NDBReaderPlugin
A reader for Genomica NDB files
(0)
NetLink
Creates node or edge hyperlinks that open other networks.
NetLink
Creates node or edge hyperlinks that open other networks.
(0)
BiNoM
Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
BiNoM
Import/Export of System Biology file formats (BioPAX level 3, SBML, CellDesigner). Analysis and manipulation of biological networks.
(17)
Commonattributes
Find attributes shared between selected nodes.
Commonattributes
Find attributes shared between selected nodes.
(0)
EnhancedSearch
Performs searches on networks based on attributes
EnhancedSearch
Performs searches on networks based on attributes
(3)
HiderSlider
Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders.
HiderSlider
Provides user sliders which can hide nodes whose continuous attribute is below threshold specied by sliders.
(0)
NamedSelection
Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.
NamedSelection
Assign name to selected nodes, and after unselection, enables user to re-select the nodes according to the name.
(0)
NeighborHighlight
Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
NeighborHighlight
Highlights the current node and all its neighboring nodes and edges when the user hovers the mouse over it.
(1)
SubnetworkCreator
Create subnetworks for disconnected graphs.
SubnetworkCreator
Create subnetworks for disconnected graphs.
(2)
