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data visualization
(78)
network analysis
(64)
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(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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non-coding RNA
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Cytoscape
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paths
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metabolite function
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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)
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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
(1)
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
(1)
supervised model
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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
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orthology
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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
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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)
Data visualization
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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
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
causalpath-cytoscape-app
Visualize CausalPath (causalpath.org) results in Cytoscape
(2) 4832 downloads
CHAT
Identify contextually relevant hubs in biological networks
CHAT
Identify contextually relevant hubs in biological networks
(2) 21893 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(28) 178962 downloads
cyBrowser
Core App: Add HTML Browser to Cytoscape
cyBrowser
Core App: Add HTML Browser to Cytoscape
(1) 52571 downloads
CyDataSeries
Add time series and the like to your networks.
CyDataSeries
Add time series and the like to your networks.
(1) 8959 downloads
CyLineUp
Visualizes data in network small multiples
CyLineUp
Visualizes data in network small multiples
(2) 8556 downloads
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
CySpanningTree
Spanning tree computation and MST heuristic for Travelling Salesman Problem
(5) 7552 downloads
cyTransFinder
Signal Transduction Pathway Finder
cyTransFinder
Signal Transduction Pathway Finder
(3) 29672 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 6052 downloads
dot-app
Import/export of Graphviz files in Cytoscape
dot-app
Import/export of Graphviz files in Cytoscape
(31) 20452 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 168271 downloads
gexf-app
Imports Graph Exchange XML Format (GEXF) files
gexf-app
Imports Graph Exchange XML Format (GEXF) files
(1) 7841 downloads
IDARE
Data Visualisation for Multi-Omics data
IDARE
Data Visualisation for Multi-Omics data
(0) 4074 downloads
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
KEGGscape
File reader and pathway visualizer for KEGG XML (KGML) files
(4) 110719 downloads
MetaNetter_2
MetaNetter_2
(1) 6424 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
Petri Net Implementation for Cytoscape
Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets
Petri Net Implementation for Cytoscape
Implements Petri nets for Cytoscape, allowing creation, loading, export and simulation of Petri nets
(4) 3467 downloads
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
PTMOracle
Co-visualisation and co-analysis of PTM and PPI data
(4) 10388 downloads
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
RenoDoI
A visual analytics approach for integrated data-knowledge networks.
(1) 4671 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
ScyNet
Visualisation of community metabolic models
ScyNet
Visualisation of community metabolic models
(1) 1991 downloads
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(36) 7431 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389210 downloads
TieDIE
Tied Diffusion Through Interacting Events
TieDIE
Tied Diffusion Through Interacting Events
(1) 6359 downloads
Venn and Euler Diagrams
Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
Venn and Euler Diagrams
Provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
(36) 27937 downloads
Worm Plot
Sequence self-similarity directed graph visualization.
Worm Plot
Sequence self-similarity directed graph visualization.
(0) 12537 downloads
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
yFiles Layout Algorithms
Highly sophisticated algorithms for arranging networks.
(30) 254228 downloads
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
boundaryLayout
A Force-Directed Network Layout with Custom Boundary Constraints
(2) 13885 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
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
cy3sbml
cy3sbml visualizes SBML models (Systems Biology Markup Language)
(3) 40890 downloads
cyChart
An interactive tool to define filters
cyChart
An interactive tool to define filters
(1) 50940 downloads
CyIsomorphism
All possible subgraph isomorphisms
CyIsomorphism
All possible subgraph isomorphisms
(4) 6023 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 50118 downloads
CyToStruct: external application hooking
Launching arbitrary external apps (such as viewers) for nodes/edges
CyToStruct: external application hooking
Launching arbitrary external apps (such as viewers) for nodes/edges
(27) 27982 downloads
D3.js Exporter
Network and Table Data Exporter for D3.js
D3.js Exporter
Network and Table Data Exporter for D3.js
(1) 15520 downloads
Diffusion
Expand node selection using network propagation algorithms
Diffusion
Expand node selection using network propagation algorithms
(35) 40526 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
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
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
HGPEC
HGPEC can effectively predict novel disease-gene and disease-disease associations and support network- and rank-based visualization
(2) 4434 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
KeyPathwayMiner
Detects highly-connected sub-networks where most genes show similar expression behavior.
KeyPathwayMiner
Detects highly-connected sub-networks where most genes show similar expression behavior.
(70) 25487 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
MSClustering
an efficient app for hierarchical clustering and phylogenetics of complex networks
MSClustering
an efficient app for hierarchical clustering and phylogenetics of complex networks
(55) 4818 downloads
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
PathInsight
An open-source application that models the effects of small binding molecules in pathways in Systems Biology Graphical Notation
(1) 3977 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
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
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
SocialNetwork
Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.
SocialNetwork
Summarizes how individuals are connected by building networks where nodes represent authors and edges represent publications.
(5) 15461 downloads
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
TiCoNE
Time Course Network Enricher is an interactive clustering method for time-series data
(73) 62671 downloads
Variation
Integrate variation and variation consequence data on biological networks.
Variation
Integrate variation and variation consequence data on biological networks.
(0) 4225 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
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
