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data visualization
(78)
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(63)
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(60)
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python
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drug
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xmlrpc
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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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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
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SLiMSearch
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SLiMFinder
(1)
SLiM
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Short linear motif
(1)
sequence self-similarity
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semantic similarity
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self-organizing map
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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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pangenomics
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orthology
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OpenBEL
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Ontology visualization
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node selection
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node.js
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network extension
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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
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Graphical Models
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graph database
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gps coordinates
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GFA
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Genetic algorithm
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Gene network validation
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Gene network
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flexibility
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Factor Graph
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evolutionary algorithm
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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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domain interaction
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diseasome
(1)
disease similarity network
(1)
Disease Ontology
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disease-disease networks
(1)
dedal
(1)
Covid-19
(1)
constrained layout
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comorbidity
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community
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clone layout
(1)
cell-fate transitions
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CDAPS
(1)
causal interactions
(1)
Cancer Progression
(1)
Cancer Evolution
(1)
blastn
(1)
Between-term similarity
(1)
Between-entity similarity
(1)
attribute summary
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assembly
(1)
alternative splicing
(1)
Visualization
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ANIMO
ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.
ANIMO
ANIMO (Analysis of Networks with Interactive MOdeling) lets you model biological networks and compare their dynamics with experimental data.
(1) 48636 downloads
clusterMaker2
Multi-algorithm clustering app for Cytoscape
clusterMaker2
Multi-algorithm clustering app for Cytoscape
(28) 178962 downloads
cymirCNV
miRNA gene correlation network visualization
cymirCNV
miRNA gene correlation network visualization
(1) 1088 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
DynDiffNet
a Cytoscape app for dynamic differential network construction, analysis and visualization
DynDiffNet
a Cytoscape app for dynamic differential network construction, analysis and visualization
(0) 1342 downloads
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
DyNetViewer
Construction, analysis, and visualization of dynamic networks in Cytoscape 3.0
(4) 13271 downloads
enhancedGraphics
A passthrough mapper for charts and gradients
enhancedGraphics
A passthrough mapper for charts and gradients
(11) 168271 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
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
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
NCMine
Finds functional modules in gene networks by Near-Clique Mining
NCMine
Finds functional modules in gene networks by Near-Clique Mining
(3) 4696 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
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
SAFE
Spatial Analysis for Functional Enrichment
SAFE
Spatial Analysis for Functional Enrichment
(0) 8591 downloads
stringApp
Import and augment Cytoscape networks from STRING
stringApp
Import and augment Cytoscape networks from STRING
(34) 389210 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
CyAnimator
Simple key-frame animation for Cytoscape
CyAnimator
Simple key-frame animation for Cytoscape
(5) 51740 downloads
cyPlot
A utility to display data plots
cyPlot
A utility to display data plots
(1) 50118 downloads
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
DeDaL
Data-driven layout (PCA...), network alignement, network morphing.
(1) 6052 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
EClerize
EClerize
(2) 2354 downloads
EntOptLayout
Relative entropy optimization based layout plugin
EntOptLayout
Relative entropy optimization based layout plugin
(6) 14337 downloads
FunCoup
Import and analyze Cytoscape networks from FunCoup
FunCoup
Import and analyze Cytoscape networks from FunCoup
(10) 2840 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
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) 34998 downloads
Omics Visualizer
Import & Visualize several data for the same node
Omics Visualizer
Import & Visualize several data for the same node
(10) 23759 downloads
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
PhosphoPath
Visualization and analysis of quantitative proteome and phosphoproteome datasets
(17) 29709 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
SemScape
Visualizes Semantic Data Landscapes
SemScape
Visualizes Semantic Data Landscapes
(36) 7431 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
