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Guide to 3.0 App Development
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data visualization
(78)
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(64)
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(63)
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(60)
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(48)
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(47)
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(39)
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python
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protein dynamics
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json
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homology
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graphviz
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entropy
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drug repositioning
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drug
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collections
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cancer genetics
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Bioconductor
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benchmark
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attribute table viewer
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active subnetwork
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xmlrpc
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variation graph
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variation consequences
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variation analysis
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variant effects
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variant-disease associations
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Triplets
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three dimensional
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temporal network
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survival analysis
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supervised model
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sql
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spatial co-expression
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spark
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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
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SABIO-RK
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Rserve
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Robustness
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Redis
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Rcaller
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random networks
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randomization
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QSLiMFinder
(1)
Probabilistic Graphical Model
(1)
Phosphoproteomics
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phenotype
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petri nets
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PCA
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pangenomics
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orthology
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optimization
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OpenBEL
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Ontology visualization
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node selection
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node mapping
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node.js
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network extension
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network controllability
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mode of action
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missing data estimation
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miRNA-gene network
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metaql
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metabolic model
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MDS
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matlab
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k-shell
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Human Phenotype Ontology
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hub analysis
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heterogeneous molecular networks
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hadoop
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graphlets
(1)
Graphical Models
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graph database
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gps coordinates
(1)
GFA
(1)
Genetic algorithm
(1)
Gene network validation
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Gene network
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Fuzzy Logic
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flexibility
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Factor Graph
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evolutionary algorithm
(1)
Evidence Collection
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ebi
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dvd
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drug similarity network
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drugome
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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)
Import
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Adj Exporter
Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks
Adj Exporter
Cytoscape app that enables AdjacencyMatrixExport formats for directed & undirected networks
(12) 14738 downloads
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
BEL Navigator
Explore OpenBEL knowledge networks within Cytoscape 3.
(0) 3220 downloads
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
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 40890 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.
(7) 15320 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 7841 downloads
InsituNet
Analysis of in situ gene expression data in terms of spatial co-expression.
InsituNet
Analysis of in situ gene expression data in terms of spatial co-expression.
(3) 8158 downloads
NDB Reader
Cytoscape app for reading Genomica NDB files
NDB Reader
Cytoscape app for reading Genomica NDB files
(0) 2838 downloads
SDP Model Builder
Cytoscape 3 app that interfaces with Selventa Development Platform
SDP Model Builder
Cytoscape 3 app that interfaces with Selventa Development Platform
(0) 2754 downloads
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
XlinkCyNET
Generate residue-to-residue connections provided by XL-MS in protein interaction networks
(4) 29585 downloads
aMatReader
App to read adjacency matrix (.mat, .adj) files
aMatReader
App to read adjacency matrix (.mat, .adj) files
(2) 17285 downloads
cdtReader
Read Cluster 3 output files into Cytoscape
cdtReader
Read Cluster 3 output files into Cytoscape
(0) 5813 downloads
CX Support
Core App: CX JSON file reader and writer
CX Support
Core App: CX JSON file reader and writer
(3) 99141 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 20452 downloads
General SPARQL
Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF
General SPARQL
Navigate SPARQL endpoints. Comes with a predefined set of SPARQL queries that work with public endpoints from EBI RDF platform and Bio2RDF
(10) 21957 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
IntAct App
Build molecular interaction networks from IntAct database. Access all details in one click.
IntAct App
Build molecular interaction networks from IntAct database. Access all details in one click.
(7) 17810 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(10) 23759 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389210 downloads
