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Guide to 3.0 App Development
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data visualization
(78)
network analysis
(64)
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(63)
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xmlrpc
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variant effects
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Triplets
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three dimensional
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supervised model
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sql
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spark
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SLiMSearch
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SLiMFinder
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SLiM
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Short linear motif
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sequence self-similarity
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semantic similarity
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sbgn
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Rserve
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Redis
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Rcaller
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random networks
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node.js
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missing data estimation
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MDS
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matlab
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k-shell
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hub analysis
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heterogeneous molecular networks
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hadoop
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graphlets
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graph database
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gps coordinates
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GFA
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flexibility
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Factor Graph
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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
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diseasome
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disease similarity network
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disease-disease networks
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dedal
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Covid-19
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constrained layout
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comorbidity
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community
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clone layout
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cell-fate transitions
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CDAPS
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causal interactions
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Cancer Progression
(1)
Cancer Evolution
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blastn
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Between-term similarity
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Between-entity similarity
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attribute summary
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assembly
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alternative splicing
(1)
Network generation
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AgilentLiteratureSearch
Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
AgilentLiteratureSearch
Mines scientific literature to find publications related to search terms and to create interaction networks based on the search result.
(28) 72640 downloads
bayelviraApp
Learning and generation of Bayesian networks.
bayelviraApp
Learning and generation of Bayesian networks.
(1) 5167 downloads
Bisogenet
Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
Bisogenet
Retrieves interactions associated with input IDs. Sophisticated UI gives links to GO, KEGG, etc.
(15) 83095 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.
(22) 45054 downloads
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 40890 downloads
cymirCNV
miRNA gene correlation network visualization
cymirCNV
miRNA gene correlation network visualization
(1) 1088 downloads
Cyni Toolbox
Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
Cyni Toolbox
Cytoscape Network Inference Toolbox puts together several tools that allow infering networks from bio data (For Cytoscape 3.1+)
(25) 23579 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 51979 downloads
ExpressionCorrelation
Makes a similarity network where nodes are genes, and edges denote highly correlated genes.
ExpressionCorrelation
Makes a similarity network where nodes are genes, and edges denote highly correlated genes.
(5) 13420 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
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
MetScape
Maps human, mouse and rat metabolomics and gene expression data to human metabolic networks and enables pathway and correlation analysis.
(25) 67568 downloads
Network Randomizer
A tool for creating random networks and comparing them to the real ones
Network Randomizer
A tool for creating random networks and comparing them to the real ones
(5) 17225 downloads
PINA4MS
Combining tissue-specific protein expression and interaction data to identify genes of functional- and disease-relevance
PINA4MS
Combining tissue-specific protein expression and interaction data to identify genes of functional- and disease-relevance
(14) 16702 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) 41374 downloads
RNA
Regulatory Network Analyzer generates/analyzes a regulatory network and states transition network and computes informations like entropy.
RNA
Regulatory Network Analyzer generates/analyzes a regulatory network and states transition network and computes informations like entropy.
(2) 14325 downloads
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
TETRAMER
A Temporal Transcription regulation modeler to predict master regulators
(26) 3335 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 109230 downloads
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
ARACNE
Network inference algorithm to address a wide range of network deconvolution problems available through Cyni
(10) 13119 downloads
BioGateway Cytoscape Plugin
An explorative network building plugin that works with the BioGateway triple store
BioGateway Cytoscape Plugin
An explorative network building plugin that works with the BioGateway triple store
(8) 13032 downloads
CluePedia
CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
CluePedia
CluePedia: A ClueGO plugin for pathway insights using integrated experimental and in silico data
(104) 232020 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).
(9) 5988 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
(14) 65281 downloads
CyNetworkBMA
Infers gene regulatory networks from expression measurements using Bayesian Model Averaging.
CyNetworkBMA
Infers gene regulatory networks from expression measurements using Bayesian Model Averaging.
(1) 4709 downloads
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
CyPath2
Pathway Commons (BioPAX L3 database) web service GUI client app
(73) 43508 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 29672 downloads
GeneMANIA
Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
GeneMANIA
Imports interaction networks from public databases from a list of genes with their annotations and putative functions.
(80) 143617 downloads
iRegulon
Detects master regulators and cis-regulatory interactions
iRegulon
Detects master regulators and cis-regulatory interactions
(12) 39367 downloads
NeDRex
Finds drug repurposing candidates and disease modules. Builds custom heterogeneous molecular networks and allows for exploration
NeDRex
Finds drug repurposing candidates and disease modules. Builds custom heterogeneous molecular networks and allows for exploration
(7) 9061 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(10) 23759 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
(23) 140514 downloads
RINalyzer
Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).
RINalyzer
Provides a number of important methods for analyzing and visualizing residue interaction networks (RINs).
(9) 8988 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389210 downloads
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
TimeNexus
Build, manage and visualize temporal multilayer networks, as well as extract active multilayer subnetworks.
(1) 2462 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
