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)
Systems biology
Search for posts about systems biology →
Ask a question about systems biology →
ANIMO
ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.
ANIMO
ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.
(1) 22319 downloads
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
CyKEGGParser
KEGG pathway tuner: accurate, tissue- and protein-protein interaction-specific pathways
(12) 36053 downloads
CytoAsp
CytoAsp
(0) 1742 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 13520 downloads
Diffany
Calculation of differential networks
Diffany
Calculation of differential networks
(4) 2503 downloads
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
(4) 6482 downloads
iCTNet2
iCTNet2
(1) 4546 downloads
Jesse
Calculate the graphlet degrees of all nodes within a graph
Jesse
Calculate the graphlet degrees of all nodes within a graph
(1) 1558 downloads
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
MCDS
Approximates the minimum connected dominating set (MCDS) of directed networks.
(13) 3325 downloads
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
(1) 1486 downloads
PEmeasure
Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)
PEmeasure
Compute links weights and assess the reliability of the links in a network (e.g. protein-protein interactions)
(9) 1964 downloads
Pesca3.0
Pesca3.0
(6) 3316 downloads
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
PSFC
Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
(1) 10060 downloads
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
ReactomeFIPlugIn
Explore Reactome pathways and search for diseases related pathways and network patterns using the Reactome functional interaction network
(21) 63780 downloads
SyncVis
Synchronous Visualizer
SyncVis
Synchronous Visualizer
(0) 1350 downloads
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
(68) 29298 downloads
CoNet
CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices.
CoNet
CoNet is a Cytoscape plugin that detects significant associations in presence/absence and abundance matrices.
(19) 24969 downloads
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
CyNDEx-2
Core App: CyNDEx-2 is a user-friendly app for browsing, importing, and exporting networks to an NDEx server.
(4) 14598 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 6929 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 2832 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) 8166 downloads
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
(1) 1925 downloads
ISMAGS
Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
ISMAGS
Enumerate all instances of a motif in a graph, making optimal use of the motif's symmetries.
(1) 6778 downloads
KDDN
Knowledge-fused Differential Dependency Network
KDDN
Knowledge-fused Differential Dependency Network
(7) 4697 downloads
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
OCSANA+
Optimal Control and Simulation of Signaling Networks from Network Analysis
(14) 487 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 13640 downloads
PEPPER
Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
PEPPER
Find meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization
(40) 18842 downloads
Petri Net Implementation for Cytoscape
Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets
Petri Net Implementation for Cytoscape
Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets
(2) 884 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 4664 downloads
Rene
Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
Rene
Regulatory Network Enhancing Plugin - ReNE allows users to enhance standard KEGG/Reactome pathways wit
(12) 20916 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(23) 1503 downloads
TMM
Predict the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways
TMM
Predict the activity of Telomere Maintenance Mechanisms from gene expression data. Contribute to improvement of TMM pathways
(0) 4274 downloads
Unsupported Plugins for Cytoscape 2.x