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Guide to 3.0 App Development
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data visualization
(78)
network analysis
(64)
network generation
(63)
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(60)
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(48)
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set visualization
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python
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protein dynamics
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non-coding RNA
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Cytoscape
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(2)
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(2)
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paths
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json
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homology
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graphviz
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entropy
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enrichment map
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drug repositioning
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drug
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data discretization
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collections
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cancer genetics
(2)
Biomedical evidence collection
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Bioconductor
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benchmark
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attribute table viewer
(2)
active subnetwork
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xmlrpc
(1)
Virtual Reality
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variation graph
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variation consequences
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variation analysis
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variant effects
(1)
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
(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
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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
(1)
Ontology visualization
(1)
node selection
(1)
node mapping
(1)
node.js
(1)
network extension
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network controllability
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mode of action
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missing data estimation
(1)
miRNA-gene network
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metaql
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metabolic model
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MDS
(1)
matlab
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k-shell
(1)
Human Phenotype Ontology
(1)
hub analysis
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heterogeneous molecular networks
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hadoop
(1)
graphlets
(1)
Graphical Models
(1)
graph database
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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)
Automation
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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
autoHGPEC
An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations
autoHGPEC
An upgrading version of HGPEC with added automation features to predict novel disease-gene and disease-disease associations
(6) 8505 downloads
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
cddApp
Integration between Cytoscape the the NCBI Conserved Domain Database
(0) 16108 downloads
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
ClueGO
Creates and visualizes a functionally grouped network of terms/pathways
(318) 403983 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
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 52571 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
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 50118 downloads
CyTargetLinker
Flexible network extension app
CyTargetLinker
Flexible network extension app
(40) 51979 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 40526 downloads
EnrichmentMap
Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
EnrichmentMap
Visualizes enrichments of pathways as an enrichment map, a network representing overlaps among enriched pathways.
(29) 168536 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
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(10) 2840 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
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
MGG
performs the microbetag workflow and visualise microbetag-annotated networks
(1) 2166 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(10) 23759 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) 25355 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
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
RWRMTN
a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
(4) 3770 downloads
setsApp
Save and manipulate sets of nodes and edges
setsApp
Save and manipulate sets of nodes and edges
(3) 22919 downloads
structureViz2
App to visualize macromolecular structures in a network context
structureViz2
App to visualize macromolecular structures in a network context
(4) 17059 downloads
WikiPathways
WikiPathways web service client and GPML file format importer
WikiPathways
WikiPathways web service client and GPML file format importer
(11) 109230 downloads
WordCloud
Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
WordCloud
Summarizes functions of interacting clusters as logos, where sizes of logo represents frequencies of these functions.
(2) 75406 downloads
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
AutoAnnotate
Finds clusters and visually annotates them with labels and groups.
(37) 78417 downloads
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
BridgeDb
Performs ID mapping using BridgeDb and other public or custom database sources.
(20) 21481 downloads
chemViz2
Cheminformatics App for Cytoscape
chemViz2
Cheminformatics App for Cytoscape
(8) 31878 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(28) 178962 downloads
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5) 51739 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 50940 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
Cyrface
Bridging Cytoscape with R
Cyrface
Bridging Cytoscape with R
(7) 6246 downloads
CytoCopteR
A Cytoscape plug-in for training logic models
CytoCopteR
A Cytoscape plug-in for training logic models
(29) 14081 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 168271 downloads
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
EnrichmentMap Pipeline Collection
Collection of Apps that are part of the EnrichmentMap pipeline workflow
(3) 30418 downloads
eXamine
A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
eXamine
A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout.
(34) 25033 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
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(4) 110718 downloads
MCODE
Clusters a given network based on topology to find densely connected regions.
MCODE
Clusters a given network based on topology to find densely connected regions.
(32) 250572 downloads
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
Motif-Discovery
It allows the user to do "Network Motif Discovery" in a fast and friendly way. It uses the G-Tries algorithm which is the fastest one.
(15) 13922 downloads
PathLinker
Reconstructs signaling pathways from protein interaction networks
PathLinker
Reconstructs signaling pathways from protein interaction networks
(14) 32684 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
RINspector
Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions
RINspector
Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions
(5) 12431 downloads
scNetViz
Single-cell RNASeq analysis in Cytoscape
scNetViz
Single-cell RNASeq analysis in Cytoscape
(1) 18166 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389210 downloads
Synapse Client
Access your data on Synapse.org from within Cyoscape
Synapse Client
Access your data on Synapse.org from within Cyoscape
(1) 6591 downloads
wk-shell-decomposition
Performs a weighted k-shell decomposition
wk-shell-decomposition
Performs a weighted k-shell decomposition
(1) 3847 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
