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bioconductor.org "GraphAndNetwork" keyword

View the packages on the bioconductor.org package registry that are tagged with the "GraphAndNetwork" keyword.

Top 2.7% on bioconductor.org
KEGGgraph 1.68.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
5 versions - Latest release: 2 months ago - 13 dependent packages - 644 thousand downloads total - 1 maintainer
MOGAMUN 1.18.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
5 versions - Latest release: 2 months ago - 7.53 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.84.0
An interface to the BOOST graph library
5 versions - Latest release: 3 months ago - 33 dependent packages - 1.68 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.86.0
graph: A package to handle graph data structures
6 versions - Latest release: 3 months ago - 101 dependent packages - 3 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.52.0
Provides plotting capabilities for R graph objects
5 versions - Latest release: 3 months ago - 61 dependent packages - 1.7 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.70.0
Gene set enrichment data structures and methods
5 versions - Latest release: 3 months ago - 49 dependent packages - 1.17 million downloads total - 1 maintainer
netZooR 1.11.0
Unified methods for the inference and analysis of gene regulatory networks
5 versions - Latest release: 3 months ago - 5.48 thousand downloads total - 109 stars on GitHub - 1 maintainer
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
5 versions - Latest release: 3 months ago - 23.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
GRENITS 1.60.0
Gene Regulatory Network Inference Using Time Series
5 versions - Latest release: 3 months ago - 27.6 thousand downloads total - 1 maintainer
poem 1.0.1
POpulation-based Evaluation Metrics
2 versions - Latest release: 2 months ago - 1.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
Pedixplorer 1.4.0
Pedigree Functions
3 versions - Latest release: 3 months ago - 3.45 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.28.1
Functions to Access and Control Cytoscape
6 versions - Latest release: 3 days ago - 15 dependent packages - 96.3 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.74.0
Tools for manipulating GO and microarrays
5 versions - Latest release: 3 months ago - 23 dependent packages - 534 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
EnrichmentBrowser 2.38.0
Seamless navigation through combined results of set-based and network-based enrichment analysis
5 versions - Latest release: 2 months ago - 5 dependent packages - 62.5 thousand downloads total - 19 stars on GitHub - 1 maintainer
hipathia 3.8.0
HiPathia: High-throughput Pathway Analysis
5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
BioNERO 1.16.0
Biological Network Reconstruction Omnibus
7 versions - Latest release: 3 months ago - 1 dependent package - 19.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
BiGGR 1.44.0
Constraint based modeling in R using metabolic reconstruction databases
5 versions - Latest release: 2 months ago - 31.6 thousand downloads total - 2 maintainers
FELLA 1.28.0
Interpretation and enrichment for metabolomics data
5 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
VennDetail 1.23.0
A package for visualization and extract details
5 versions - Latest release: 2 months ago - 18 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
biocGraph 1.70.0
Graph examples and use cases in Bioinformatics
5 versions - Latest release: 3 months ago - 1 dependent package - 59.5 thousand downloads total - 1 maintainer
DEsubs 1.34.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...
5 versions - Latest release: 3 months ago - 15.8 thousand downloads total - 2 maintainers
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
5 versions - Latest release: 2 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
spqn 1.20.0
Spatial quantile normalization
5 versions - Latest release: 3 months ago - 7.91 thousand downloads total - 5 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.28.1
Reproducible GSEA Benchmarking
6 versions - Latest release: about 2 months ago - 2 dependent packages - 14.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
syntenet 1.10.0
Inference And Analysis Of Synteny Networks
8 versions - Latest release: 3 months ago - 1 dependent package - 7.84 thousand downloads total - 30 stars on GitHub - 1 maintainer
netboost 2.16.0
Network Analysis Supported by Boosting
5 versions - Latest release: 3 months ago - 8.54 thousand downloads total - 1 maintainer
DeepPINCS 1.16.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
5 versions - Latest release: 3 months ago - 2 dependent packages - 7.41 thousand downloads total - 1 maintainer
plotGrouper 1.26.0
Shiny app GUI wrapper for ggplot with built-in statistical analysis
5 versions - Latest release: 2 months ago - 9.69 thousand downloads total - 6 stars on GitHub - 1 maintainer
GWENA 1.18.0
Pipeline for augmented co-expression analysis
5 versions - Latest release: 3 months ago - 13.6 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
hyperdraw 1.60.0
Visualizing Hypergaphs
5 versions - Latest release: 3 months ago - 1 dependent package - 38.1 thousand downloads total - 1 maintainer
OmnipathR 3.16.0
OmniPath web service client and more
7 versions - Latest release: 3 months ago - 3 dependent packages - 44 thousand downloads total - 1 maintainer
rScudo 1.24.0
Signature-based Clustering for Diagnostic Purposes
6 versions - Latest release: 3 months ago - 9.68 thousand downloads total - 4 stars on GitHub - 1 maintainer
diffuStats 1.28.0
Diffusion scores on biological networks
5 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 1 maintainer
pareg 1.12.0
Pathway enrichment using a regularized regression approach
5 versions - Latest release: 3 months ago - 4.14 thousand downloads total - 7 stars on GitHub - 1 maintainer
Rigraphlib 1.0.0
igraph library as an R package
1 version - Latest release: 3 months ago - 2.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
IMMAN 1.28.0
Interlog protein network reconstruction by Mapping and Mining ANalysis
5 versions - Latest release: 3 months ago - 11.4 thousand downloads total - 1 maintainer
ReactomeGraph4R 1.16.0
Interface for the Reactome Graph Database
6 versions - Latest release: 3 months ago - 4.21 thousand downloads total - 6 stars on GitHub - 1 maintainer
ANF 1.30.0
Affinity Network Fusion for Complex Patient Clustering
6 versions - Latest release: 3 months ago - 14.9 thousand downloads total - 1 maintainer
TMSig 1.2.0
Tools for Molecular Signatures
2 versions - Latest release: 3 months ago - 1.72 thousand downloads total - 4 stars on GitHub - 1 maintainer
gsean 1.28.0
Gene Set Enrichment Analysis with Networks
5 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment
5 versions - Latest release: 3 months ago - 11 dependent packages - 295 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
keggorthology 2.60.0
graph support for KO, KEGG Orthology
5 versions - Latest release: 3 months ago - 1 dependent package - 45.3 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.56.0
Pathways from the NCI Pathways Database
5 versions - Latest release: 3 months ago - 1 dependent package - 31 thousand downloads total - 1 maintainer
PhenoGeneRanker 1.16.0
PhenoGeneRanker: A gene and phenotype prioritization tool
5 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
apComplex 2.74.0
Estimate protein complex membership using AP-MS protein data
5 versions - Latest release: 3 months ago - 48.7 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
rsbml 2.66.0
R support for SBML, using libsbml
5 versions - Latest release: 3 months ago - 3 dependent packages - 59.8 thousand downloads total - 1 maintainer
tidysbml 1.2.0
Extract SBML's data into dataframes
2 versions - Latest release: 3 months ago - 1.76 thousand downloads total - 1 stars on GitHub - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
5 versions - Latest release: 3 months ago - 1 dependent package - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
BioMVCClass 1.76.0
Model-View-Controller (MVC) Classes That Use Biobase
5 versions - Latest release: 3 months ago - 39.9 thousand downloads total - 1 maintainer
GeneNetworkBuilder 1.50.0
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-s...
5 versions - Latest release: 3 months ago - 28.7 thousand downloads total - 1 maintainer
ternarynet 1.52.0
Ternary Network Estimation
5 versions - Latest release: 3 months ago - 23.2 thousand downloads total - 1 maintainer
Top 4.6% on bioconductor.org
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
5 versions - Latest release: 3 months ago - 1 dependent package - 61.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
RITAN 1.32.0
Rapid Integration of Term Annotation and Network resources
5 versions - Latest release: 3 months ago - 13.4 thousand downloads total - 1 maintainer
QuaternaryProd 1.42.0
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
5 versions - Latest release: 3 months ago - 16.2 thousand downloads total - 1 maintainer
Pigengene 1.34.0
Infers biological signatures from gene expression data
5 versions - Latest release: 3 months ago - 1 dependent package - 18.5 thousand downloads total - 1 maintainer
rTRMui 1.46.0
A shiny user interface for rTRM
5 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
nethet 1.40.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
5 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 2 maintainers
netresponse 1.68.0
Functional Network Analysis
5 versions - Latest release: 3 months ago - 30 thousand downloads total - 3 stars on GitHub - 1 maintainer
sparsenetgls 1.26.0
Using Gaussian graphical structue learning estimation in generalized least squared regression for...
5 versions - Latest release: 3 months ago - 9.08 thousand downloads total - 1 maintainer
TreeAndLeaf 1.20.0
Displaying binary trees with focus on dendrogram leaves
5 versions - Latest release: 3 months ago - 1 dependent package - 11.8 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MVCClass 1.82.0
Model-View-Controller (MVC) Classes
5 versions - Latest release: 3 months ago - 1 dependent package - 37.4 thousand downloads total - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data
5 versions - Latest release: 3 months ago - 5.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
BatchQC 2.4.0
Batch Effects Quality Control Software
5 versions - Latest release: 3 months ago - 25.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
PathoStat 1.34.0
PathoStat Statistical Microbiome Analysis Package
5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 8 stars on GitHub - 2 maintainers
epiregulon.extra 1.4.0
Companion package to epiregulon with additional plotting, differential and graph functions
6 versions - Latest release: 3 months ago - 3.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
fobitools 1.16.0
Tools for Manipulating the FOBI Ontology
5 versions - Latest release: 3 months ago - 6.81 thousand downloads total - 1 stars on GitHub - 1 maintainer
goSorensen 1.10.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
5 versions - Latest release: 3 months ago - 5.11 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.66.0
Mutual Information NETworks
5 versions - Latest release: 3 months ago - 9 dependent packages - 138 thousand downloads total - 1 maintainer
HGC 1.16.0
A fast hierarchical graph-based clustering method
5 versions - Latest release: 3 months ago - 6.96 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
RTN 2.32.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
5 versions - Latest release: 3 months ago - 3 dependent packages - 34.9 thousand downloads total - 1 maintainer
DART 1.56.0
Denoising Algorithm based on Relevance network Topology
5 versions - Latest release: 3 months ago - 29.2 thousand downloads total - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions
5 versions - Latest release: 3 months ago - 7.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
DEGraph 1.60.0
Two-sample tests on a graph
5 versions - Latest release: 3 months ago - 1 dependent package - 30.8 thousand downloads total - 1 maintainer
SGCP 1.8.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
7 versions - Latest release: 3 months ago - 5.33 thousand downloads total - 2 stars on GitHub - 1 maintainer
COSNet 1.42.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
5 versions - Latest release: 3 months ago - 18.6 thousand downloads total - 1 stars on GitHub
BioNAR 1.10.0
Biological Network Analysis in R
10 versions - Latest release: 3 months ago - 5.59 thousand downloads total - 1 maintainer
pairkat 1.14.0
PaIRKAT
5 versions - Latest release: 3 months ago - 6 thousand downloads total - 0 stars on GitHub - 1 maintainer
GRaNIE 1.12.0
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using sing...
5 versions - Latest release: 3 months ago - 7.59 thousand downloads total - 1 maintainer
PPInfer 1.34.0
Inferring functionally related proteins using protein interaction networks
5 versions - Latest release: 3 months ago - 1 dependent package - 17.2 thousand downloads total - 1 maintainer
TRONCO 2.40.0
TRONCO, an R package for TRanslational ONCOlogy
5 versions - Latest release: 3 months ago - 21.2 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.76.0
Render molecular pathways
5 versions - Latest release: 3 months ago - 35 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses
6 versions - Latest release: 3 months ago - 1 dependent package - 34.5 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAT 1.80.0
Graph Theoretic Association Tests
5 versions - Latest release: 3 months ago - 35 thousand downloads total - 1 maintainer
dce 1.13.0
Pathway Enrichment Based on Differential Causal Effects
4 versions - Latest release: 8 months ago - 6.41 thousand downloads total - 13 stars on GitHub - 1 maintainer
CEMiTool 1.32.0
Co-expression Modules identification Tool
6 versions - Latest release: 3 months ago - 33.9 thousand downloads total - 1 maintainer
RGraph2js 1.36.0
Convert a Graph into a D3js Script
5 versions - Latest release: 3 months ago - 14.3 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.48.0
a tool set for pathway based data integration and visualization
5 versions - Latest release: 3 months ago - 9 dependent packages - 594 thousand downloads total - 41 stars on GitHub - 1 maintainer
Top 8.1% on bioconductor.org
SBMLR 2.4.0
SBML-R Interface and Analysis Tools
5 versions - Latest release: 3 months ago - 34.4 thousand downloads total - 1 maintainer
PIUMA 1.4.0
Phenotypes Identification Using Mapper from topological data Analysis
3 versions - Latest release: 3 months ago - 3.18 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
GraphAlignment 1.72.0
GraphAlignment
5 versions - Latest release: 3 months ago - 33.3 thousand downloads total - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
14 versions - Latest release: 28 days ago - 11.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
magrene 1.10.0
Motif Analysis In Gene Regulatory Networks
5 versions - Latest release: 3 months ago - 4.74 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaboSignal 1.38.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
6 versions - Latest release: 3 months ago - 18.5 thousand downloads total - 2 maintainers
pandaR 1.40.0
PANDA Algorithm
5 versions - Latest release: 3 months ago - 1 dependent package - 21.8 thousand downloads total - 2 maintainers
EGAD 1.36.0
Extending guilt by association by degree
5 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
glmSparseNet 1.26.0
Network Centrality Metrics for Elastic-Net Regularized Models
6 versions - Latest release: 3 months ago - 80.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
ClusterFoldSimilarity 1.4.0
Calculate similarity of clusters from different single cell samples using foldchanges
3 versions - Latest release: 3 months ago - 3.3 thousand downloads total - 1 maintainer
R3CPET 1.40.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
6 versions - Latest release: 3 months ago - 16.9 thousand downloads total - 3 stars on GitHub - 1 maintainer
splineTimeR 1.36.0
Time-course differential gene expression data analysis using spline regression models followed by...
5 versions - Latest release: 3 months ago - 16.7 thousand downloads total - 2 maintainers
paircompviz 1.46.0
Multiple comparison test visualization
5 versions - Latest release: 3 months ago - 21.4 thousand downloads total - 1 maintainer
Related Keywords
Software 149 Network 90 GeneExpression 53 Pathways 46 Visualization 36 NetworkInference 36 SystemsBiology 32 Clustering 29 Microarray 29 NetworkEnrichment 27 GeneSetEnrichment 27 RNASeq 25 DifferentialExpression 25 KEGG 22 ImmunoOncology 21 Transcription 16 GeneRegulation 16 Transcriptomics 16 Metabolomics 14 Sequencing 14 Regression 13 Classification 12 StatisticalMethod 12 BiomedicalInformatics 11 GO 10 Genetics 10 Reactome 10 SingleCell 10 Proteomics 9 ThirdPartyClient 9 DimensionReduction 9 GeneTarget 9 DataImport 8 Normalization 8 Annotation 8 Bayesian 7 bioinformatics 7 mRNAMicroarray 6 CellBiology 6 r 6 QualityControl 6 GenePrediction 6 DataRepresentation 6 GeneSignaling 5 Preprocessing 5 MultipleComparison 5 FunctionalGenomics 5 Survival 5 PrincipalComponent 5 GenomeWideAssociation 4 GeneticVariability 4 ATACSeq 4 Infrastructure 4 r-package 4 SNP 4 GUI 4 NeuralNetwork 3 TimeCourse 3 DecisionTree 3 TwoChannel 3 bioconductor 3 MassSpectrometry 3 FeatureExtraction 3 HiC 2 systems-biology 2 enrichment-analysis 2 network-analysis 2 genomics 2 ReportWriting 2 gene-regulatory-network 2 BatchEffect 2 CopyNumberVariation 2 pathways 2 DNAMethylation 2 networks 2 Epigenetics 2 ChIPSeq 2 DNASeq 2 SomaticMutation 2 Phylogenetics 2 CellBasedAssays 2 network-science 2 Spatial 2 rstats 2 genecoexpressionnetwork 1 transcription-facto 1 dirichlet-process-mixtures 1 chromatin-interaction 1 chia-pet 1 FunctionalPrediction 1 network-motifs 1 motif-analysis 1 MotifDiscovery 1 TissueMicroarray 1 causality 1 OneChannel 1 graphs 1 networkclustering 1 unsupervised-learning 1 semi-supervised-learning 1