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Guide to 3.0 App Development
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data visualization
(78)
network analysis
(64)
network generation
(63)
graph analysis
(60)
automation
(48)
online data import
(47)
clustering
(39)
integrated analysis
(37)
systems biology
(33)
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(32)
utility
(32)
enrichment analysis
(32)
data integration
(27)
core app
(25)
annotation
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pathway database
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ontology analysis
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Network structure
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export
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pathway
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networks
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network manipulation
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disease
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cancer data analysis
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network partitioning
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gene regulation
(8)
database
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animation
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molecular structure
(7)
linked data
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grouping
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gene-disease association
(7)
Connection sub-graph discovery
(7)
centrality analysis
(7)
3d visualization
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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
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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)
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)
RDF
(2)
protein structure analysis
(2)
prognostic network module
(2)
Phylogenetic Trees
(2)
Pathway acitivity analysis
(2)
paths
(2)
network view
(2)
network validation
(2)
network medicine
(2)
Neo4j
(2)
mutation analysis
(2)
multilayer network
(2)
motif detection
(2)
molecular dynamics
(2)
module detection
(2)
metabolite function
(2)
logic modelling
(2)
json
(2)
Interactive search
(2)
Interactive Layout
(2)
homology
(2)
GWAS
(2)
Greedy algorithm
(2)
graphviz
(2)
GPU Computing
(2)
Gene Ontology
(2)
Gene network analysis
(2)
Feedforward loop
(2)
Feedback loop
(2)
Euler diagram
(2)
entropy
(2)
enrichment map
(2)
drug repositioning
(2)
drug
(2)
data discretization
(2)
collections
(2)
cancer genetics
(2)
Biomedical evidence collection
(2)
Bioconductor
(2)
benchmark
(2)
attribute table viewer
(2)
active subnetwork
(2)
xmlrpc
(1)
Virtual Reality
(1)
variation graph
(1)
variation consequences
(1)
variation analysis
(1)
variant effects
(1)
variant-disease associations
(1)
Triplets
(1)
three dimensional
(1)
temporal network
(1)
survival analysis
(1)
supervised model
(1)
sql
(1)
spatial co-expression
(1)
spark
(1)
Software Dependency Graphs
(1)
SLiMSearch
(1)
SLiMFinder
(1)
SLiM
(1)
Short linear motif
(1)
sequence self-similarity
(1)
semantic similarity
(1)
self-organizing map
(1)
sbgn
(1)
SABIO-RK
(1)
Rserve
(1)
Robustness
(1)
Redis
(1)
Rcaller
(1)
random networks
(1)
randomization
(1)
QSLiMFinder
(1)
Probabilistic Graphical Model
(1)
Phosphoproteomics
(1)
phenotype
(1)
petri nets
(1)
PCA
(1)
pangenomics
(1)
orthology
(1)
optimization
(1)
OpenBEL
(1)
Ontology visualization
(1)
node selection
(1)
node mapping
(1)
node.js
(1)
network extension
(1)
network controllability
(1)
mode of action
(1)
missing data estimation
(1)
miRNA-gene network
(1)
metaql
(1)
metabolic model
(1)
MDS
(1)
matlab
(1)
k-shell
(1)
Human Phenotype Ontology
(1)
hub analysis
(1)
heterogeneous molecular networks
(1)
hadoop
(1)
graphlets
(1)
Graphical Models
(1)
graph database
(1)
gps coordinates
(1)
GFA
(1)
Genetic algorithm
(1)
Gene network validation
(1)
Gene network
(1)
Fuzzy Logic
(1)
flexibility
(1)
Factor Graph
(1)
evolutionary algorithm
(1)
Evidence Collection
(1)
ebi
(1)
dvd
(1)
drug similarity network
(1)
drugome
(1)
drug-disease association
(1)
domain interaction
(1)
diseasome
(1)
disease similarity network
(1)
Disease Ontology
(1)
disease-disease networks
(1)
dedal
(1)
Covid-19
(1)
constrained layout
(1)
comorbidity
(1)
community
(1)
clone layout
(1)
cell-fate transitions
(1)
CDAPS
(1)
causal interactions
(1)
Cancer Progression
(1)
Cancer Evolution
(1)
blastn
(1)
Between-term similarity
(1)
Between-entity similarity
(1)
attribute summary
(1)
assembly
(1)
alternative splicing
(1)
Core app
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aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2) 17285 downloads
BioPAX Reader
Core App: Provides support for reading BioPAX files in Cytoscape
BioPAX Reader
Core App: Provides support for reading BioPAX files in Cytoscape
(41) 16957 downloads
Core Apps
Core App: Set of apps packaged with the regular Cytoscape distribution. You do not need to install these separately.
Core Apps
Core App: Set of apps packaged with the regular Cytoscape distribution. You do not need to install these separately.
(1) 4520 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 52571 downloads
CyCL
Core App: Provides OpenCL support for Cytoscape
CyCL
Core App: Provides OpenCL support for Cytoscape
(0) 31912 downloads
cyREST
Core App: Language-agnostic RESTful API
cyREST
Core App: Language-agnostic RESTful API
(4) 159989 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 168271 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1) 36765 downloads
JSON Support
Core App: Provides support for reading/writing Cytoscape.js JSON files in Cytoscape
JSON Support
Core App: Provides support for reading/writing Cytoscape.js JSON files in Cytoscape
(1) 18159 downloads
mapSourceAndTarget
mapSourceAndTarget
(2) 1971 downloads
Network Merge
Core App: Provides Cytoscape's Network Merge tool
Network Merge
Core App: Provides Cytoscape's Network Merge tool
(1) 46145 downloads
PSICQUIC Web Service Client
Core App: Provides support for PSICQUIC web service in Cytoscape
PSICQUIC Web Service Client
Core App: Provides support for PSICQUIC web service in Cytoscape
(1) 9999 downloads
SBML Reader
Core App: Provides support for reading SBML files in Cytoscape
SBML Reader
Core App: Provides support for reading SBML files in Cytoscape
(1) 20548 downloads
Biomart Web Service Client
Core App: Provides support for Biomart web service in Cytoscape
Biomart Web Service Client
Core App: Provides support for Biomart web service in Cytoscape
(0) 12060 downloads
copycatLayout
Clone a network view layout by mapping node column values
copycatLayout
Clone a network view layout by mapping node column values
(1) 14194 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 99141 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 50940 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) 69184 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 40526 downloads
EnrichmentTable
Creates a new table for performing, storing and viewing functional enrichment analysis
EnrichmentTable
Creates a new table for performing, storing and viewing functional enrichment analysis
(7) 21459 downloads
ID Mapper
A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.
ID Mapper
A plug-in to the BridgeDB service to provide identifier lookup. Right-click on a column header to use the "Map Column" command.
(1) 20096 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4) 11066 downloads
NetworkAnalyzer
Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)
NetworkAnalyzer
Calculates topological properties of a network (degree distribution, clustering coefficients, centrality, etc.)
(12) 81178 downloads
OpenCL Prefuse Layout
Core App: Provides faster OpenCL-based version of Cytoscape Prefuse layout
OpenCL Prefuse Layout
Core App: Provides faster OpenCL-based version of Cytoscape Prefuse layout
(0) 29980 downloads
PSI-MI Reader
Core App: Provides support for reading PSI-MI files in Cytoscape
PSI-MI Reader
Core App: Provides support for reading PSI-MI files in Cytoscape
(0) 11179 downloads
