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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)
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(27)
core app
(25)
annotation
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pathway database
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ontology analysis
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gene expression
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interaction database
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functional analysis
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Network structure
(14)
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regulatory networks
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network dynamics
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Topology
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heat map visualization
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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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attribute generation
(8)
animation
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molecular structure
(7)
linked data
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ID mapping
(7)
grouping
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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
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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)
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) 4663 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 52571 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 29672 downloads
FileTransfer
File system proxy for remote Jupyter Notebooks
FileTransfer
File system proxy for remote Jupyter Notebooks
(1) 36765 downloads
GenomeSpace
Enables communication with GenomeSpace
GenomeSpace
Enables communication with GenomeSpace
(5) 9200 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) 9293 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) 34996 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) 7594 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 22919 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) 6501 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 6023 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 20452 downloads
FileWatcher
An App to Link Networks with Excel Files
FileWatcher
An App to Link Networks with Excel Files
(0) 4881 downloads
Highlighter
Highlight and select nodes based on shared custom node annotations.
Highlighter
Highlight and select nodes based on shared custom node annotations.
(1) 3672 downloads
Largest Subnetwork
Selects the largest connected component in a network
Largest Subnetwork
Selects the largest connected component in a network
(4) 11066 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) 3534 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) 15901 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) 11693 downloads
