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data visualization
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export
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simulation
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Random walk with restart algorithm
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network learning
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microarrays
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gene co-expression
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shortest paths
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R
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python
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protein dynamics
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post-translational modification
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Pathway analysis
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network repository
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inference
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graph clustering
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genome visualization
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Layout
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boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 10937 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 9543 downloads
CyFinder
CyFinder
(3) 3430 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(13) 22932 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(6) 11325 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1) 4722 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 18000 downloads
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
CoordinatesLayout
Load a graph with a layout that locates its nodes according to predefined 2D coordinates (typically GPS coordinates).
(9) 5063 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(3) 17434 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 4978 downloads
EClerize
EClerize
(2) 1695 downloads
GOlorize
Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.
GOlorize
Uses Gene Ontology (GO) categories to direct the network graph layout process and to emphasize nodes biological function.
(2) 15273 downloads
polyLayout
Simple n-partide layout algorithm that organizes categories along sides of regular polygons
polyLayout
Simple n-partide layout algorithm that organizes categories along sides of regular polygons
(1) 4230 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(29) 197734 downloads
Unsupported Plugins for Cytoscape 2.x
BiLayout
Finds a bipartite network for two sets of user-selected nodes and performs layout.
BiLayout
Finds a bipartite network for two sets of user-selected nodes and performs layout.
(8)
GPML-Plugin
Enables import of GPML file via import menu.
GPML-Plugin
Enables import of GPML file via import menu.
(10)
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
KGMLReader
File reader and pathway visualizer for KEGG XML (KGML) files
(61)
MultiLevelLayout
Layout algorithm for hierarchical biological networks.
MultiLevelLayout
Layout algorithm for hierarchical biological networks.
(2)
FM3
Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005.
FM3
Performs one of the fastest multilevel force directed Layouts called FM3 Layout introduced by Hachul S et al 2005.
(0)
IgraphPlugin
Brings some functionality of Igraph such as layouts into Cytoscape. Mac only.
IgraphPlugin
Brings some functionality of Igraph such as layouts into Cytoscape. Mac only.
(4)
Mosaic
Systematically partition the given graph, and layout and color nodes based on GO terms.
Mosaic
Systematically partition the given graph, and layout and color nodes based on GO terms.
(19)
ReOrientPlugin
Layouts node positions according to reference Cytoscape session file.
ReOrientPlugin
Layouts node positions according to reference Cytoscape session file.
(1)
