Submit an App
Submit a 3.0 App
Guide to 3.0 App Development
Sign In
All Apps
Categories
collections
(4)
data visualization
(77)
network generation
(61)
network analysis
(59)
graph analysis
(59)
online data import
(47)
automation
(45)
integrated analysis
(38)
clustering
(38)
utility
(32)
systems biology
(32)
enrichment analysis
(31)
visualization
(29)
data integration
(28)
layout
(22)
core app
(21)
annotation
(21)
pathway database
(18)
ontology analysis
(18)
import
(18)
gene expression
(18)
network comparison
(16)
local data import
(16)
functional analysis
(16)
interaction database
(15)
PPI-network
(14)
scripting
(13)
Network structure
(13)
network dynamics
(12)
GO annotation
(12)
regulatory networks
(11)
Topology
(10)
pathway
(10)
network inference
(10)
heat map visualization
(10)
networks
(9)
network manipulation
(9)
export
(9)
cancer data analysis
(9)
gene regulation
(8)
functional module detection
(8)
disease
(8)
database
(8)
attribute generation
(8)
animation
(8)
network partitioning
(7)
molecular structure
(7)
linked data
(7)
ID mapping
(7)
grouping
(7)
gene-disease association
(7)
Connection sub-graph discovery
(7)
simulation
(6)
Random walk with restart algorithm
(6)
network learning
(6)
microarrays
(6)
centrality analysis
(6)
social network analysis
(5)
shortest paths
(5)
sequence similarity
(5)
R
(5)
Protein complex
(5)
Pathway finding
(5)
network alignment
(5)
Gene prioritization
(5)
gene co-expression
(5)
data manipulation
(5)
cluster visualization
(5)
3d visualization
(5)
structural biology
(4)
SPARQL
(4)
signaling
(4)
SBML
(4)
literature mining
(4)
kegg
(4)
JavaScript
(4)
gene function prediction
(4)
flux analysis
(4)
variant analysis
(3)
set visualization
(3)
set analysis
(3)
search
(3)
python
(3)
protein dynamics
(3)
post-translational modification
(3)
pathway reconstruction
(3)
network repository
(3)
inference
(3)
genome visualization
(3)
disease-disease association
(3)
Cancer
(3)
Boolean Network
(3)
bayesian networks
(3)
Layout
Search for posts about layout →
Ask a question about layout →
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 7627 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 6853 downloads
CyFinder
CyFinder
(2) 1910 downloads
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
DynNetwork
Visualize dynamic networks in Cytoscape 3.0
(12) 19888 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(5) 9080 downloads
layoutSaver
Map node positions from one network to another
layoutSaver
Map node positions from one network to another
(1) 3645 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 14369 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).
(6) 3816 downloads
Cy3D
Simple 3D Network Renderer App
Cy3D
Simple 3D Network Renderer App
(2) 12879 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 3961 downloads
EClerize
EClerize
(2) 1242 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) 12690 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) 3148 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(25) 121760 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)
