bioconductor.org "Network" keyword
View the packages on the bioconductor.org package registry that are tagged with the "Network" keyword.
Top 1.4% on bioconductor.org
5 versions - Latest release: 5 months ago - 33 dependent packages - 1.72 million downloads total - 1 maintainer
RBGL 1.84.0
An interface to the BOOST graph library5 versions - Latest release: 5 months ago - 33 dependent packages - 1.72 million downloads total - 1 maintainer
Top 2.7% on bioconductor.org
5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.54.0
GRAPH Interaction from pathway Topological Environment5 versions - Latest release: 4 months ago - 11 dependent packages - 310 thousand downloads total - 8 stars on GitHub - 1 maintainer
BioNetStat 1.24.0 removed
Biological Network Analysis3 versions - Latest release: over 1 year ago - 9.35 thousand downloads total - 7 stars on GitHub - 1 maintainer
epiregulon 1.4.0
Gene regulatory network inference from single cell epigenomic data4 versions - Latest release: 4 months ago - 1 dependent package - 3.64 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
6 versions - Latest release: 4 months ago - 4 dependent packages - 58.1 thousand downloads total - 1 maintainer
RedeR 3.4.0
Interactive visualization and manipulation of nested networks6 versions - Latest release: 4 months ago - 4 dependent packages - 58.1 thousand downloads total - 1 maintainer
nempi 1.16.0
Inferring unobserved perturbations from gene expression data5 versions - Latest release: 4 months ago - 7.12 thousand downloads total - 2 stars on GitHub - 1 maintainer
BioCor 1.32.0
Functional similarities5 versions - Latest release: 4 months ago - 19 thousand downloads total - 14 stars on GitHub - 1 maintainer
KinSwingR 1.26.0
KinSwingR: network-based kinase activity prediction5 versions - Latest release: 4 months ago - 10.2 thousand downloads total - 1 maintainer
SPEM 1.48.0
S-system parameter estimation method5 versions - Latest release: 4 months ago - 1 dependent package - 25.1 thousand downloads total - 1 maintainer
bnem 1.16.0
Training of logical models from indirect measurements of perturbation experiments5 versions - Latest release: 4 months ago - 7.52 thousand downloads total - 2 stars on GitHub - 1 maintainer
pathlinkR 1.4.0
Analyze and interpret RNA-Seq results4 versions - Latest release: 4 months ago - 4.63 thousand downloads total - 29 stars on GitHub - 1 maintainer
MSstatsBioNet 1.0.0
Network Analysis for MS-based Proteomics Experiments1 version - Latest release: 5 months ago - 1.44 thousand downloads total - 2 stars on GitHub - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions14 versions - Latest release: 2 months ago - 12.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
COSNet 1.42.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings5 versions - Latest release: 4 months ago - 19.4 thousand downloads total - 1 stars on GitHub
CausalR 1.40.0
Causal network analysis methods5 versions - Latest release: 4 months ago - 18.2 thousand downloads total - 2 maintainers
RGMQL 1.28.0
GenoMetric Query Language for R/Bioconductor6 versions - Latest release: 4 months ago - 8.43 thousand downloads total - 1 maintainer
doubletrouble 1.8.1
Identification and classification of duplicated genes12 versions - Latest release: about 1 month ago - 6.3 thousand downloads total - 27 stars on GitHub - 1 maintainer
glmSparseNet 1.26.0
Network Centrality Metrics for Elastic-Net Regularized Models6 versions - Latest release: 4 months ago - 105 thousand downloads total - 3 stars on GitHub - 1 maintainer
netprioR 1.34.0
A model for network-based prioritisation of genes5 versions - Latest release: 4 months ago - 13.1 thousand downloads total - 1 maintainer
wppi 1.16.0
Weighting protein-protein interactions5 versions - Latest release: 4 months ago - 8.72 thousand downloads total - 1 stars on GitHub - 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: 5 months ago - 5.87 thousand downloads total - 2 stars on GitHub - 1 maintainer
XINA 1.26.0
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis5 versions - Latest release: 4 months ago - 12.6 thousand downloads total - 1 maintainer
AMOUNTAIN 1.34.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...5 versions - Latest release: 4 months ago - 1 dependent package - 20.3 thousand downloads total - 1 maintainer
bioCancer 1.36.0
Interactive Multi-Omics Cancers Data Visualization and Analysis7 versions - Latest release: 4 months ago - 17.6 thousand downloads total - 21 stars on GitHub - 1 maintainer
rrvgo 1.20.0
Reduce + Visualize GO7 versions - Latest release: 5 months ago - 31.5 thousand downloads total - 31 stars on GitHub - 1 maintainer
transomics2cytoscape 1.18.0
A tool set for 3D Trans-Omic network visualization with Cytoscape6 versions - Latest release: 4 months ago - 8.35 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 4 months ago - 7 dependent packages - 484 thousand downloads total - 331 stars on GitHub - 2 maintainers
TCGAbiolinks 2.36.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data7 versions - Latest release: 4 months ago - 7 dependent packages - 484 thousand downloads total - 331 stars on GitHub - 2 maintainers
NetPathMiner 1.44.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization5 versions - Latest release: 5 months ago - 24 thousand downloads total - 9 stars on GitHub - 1 maintainer
vissE 1.16.0
Visualising Set Enrichment Analysis Results5 versions - Latest release: 4 months ago - 9.45 thousand downloads total - 18 stars on GitHub - 1 maintainer
martini 1.28.0
GWAS Incorporating Networks5 versions - Latest release: 4 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Moonlight2R 1.6.0
Identify oncogenes and tumor suppressor genes from omics data4 versions - Latest release: 5 months ago - 4.63 thousand downloads total - 5 stars on GitHub - 1 maintainer
ReducedExperiment 1.0.2
Containers and tools for dimensionally-reduced -omics representations2 versions - Latest release: 2 months ago - 1.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
BulkSignalR 1.0.4
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...3 versions - Latest release: 9 days ago - 2.08 thousand downloads total - 1 stars on GitHub - 1 maintainer
CARNIVAL 2.18.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...5 versions - Latest release: 4 months ago - 2 dependent packages - 15.8 thousand downloads total - 59 stars on GitHub - 1 maintainer
KBoost 1.16.0
Inference of gene regulatory networks from gene expression data5 versions - Latest release: 4 months ago - 6.45 thousand downloads total - 4 stars on GitHub - 1 maintainer
ceRNAnetsim 1.20.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)6 versions - Latest release: 4 months ago - 8.05 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
5 versions - Latest release: 4 months ago - 34 thousand downloads total - 1 maintainer
GraphAlignment 1.72.0
GraphAlignment5 versions - Latest release: 4 months ago - 34 thousand downloads total - 1 maintainer
pandaR 1.40.0
PANDA Algorithm5 versions - Latest release: 4 months ago - 1 dependent package - 22.5 thousand downloads total - 2 maintainers
SANTA 2.44.0
Spatial Analysis of Network Associations5 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
5 versions - Latest release: 5 months ago - 2 dependent packages - 107 thousand downloads total - 1 maintainer
GENIE3 1.30.0
GEne Network Inference with Ensemble of trees5 versions - Latest release: 5 months ago - 2 dependent packages - 107 thousand downloads total - 1 maintainer
mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis5 versions - Latest release: 5 months ago - 17.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
RGraph2js 1.36.0
Convert a Graph into a D3js Script5 versions - Latest release: 4 months ago - 15 thousand downloads total - 1 maintainer
EGAD 1.36.0
Extending guilt by association by degree5 versions - Latest release: 4 months ago - 18.5 thousand downloads total - 1 maintainer
MODA 1.34.0
MODA: MOdule Differential Analysis for weighted gene co-expression network5 versions - Latest release: 4 months ago - 16 thousand downloads total - 1 maintainer
CEMiTool 1.32.0
Co-expression Modules identification Tool6 versions - Latest release: 4 months ago - 34.8 thousand downloads total - 1 maintainer
mosbi 1.14.0
Molecular Signature identification using Biclustering5 versions - Latest release: 4 months ago - 6.82 thousand downloads total - 1 maintainer
epiregulon.extra 1.4.0
Companion package to epiregulon with additional plotting, differential and graph functions6 versions - Latest release: 4 months ago - 3.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
MethylMix 2.38.0
MethylMix: Identifying methylation driven cancer genes5 versions - Latest release: 4 months ago - 28 thousand downloads total - 1 maintainer
miaSim 1.14.0
Microbiome Data Simulation5 versions - Latest release: 4 months ago - 7.74 thousand downloads total - 22 stars on GitHub - 1 maintainer
rWikiPathways 1.28.0
rWikiPathways - R client library for the WikiPathways API5 versions - Latest release: 5 months ago - 5 dependent packages - 69.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
tidysbml 1.2.0
Extract SBML's data into dataframes2 versions - Latest release: 4 months ago - 2.27 thousand downloads total - 1 stars on GitHub - 1 maintainer
HPiP 1.14.0
Host-Pathogen Interaction Prediction5 versions - Latest release: 4 months ago - 6.68 thousand downloads total - 3 stars on GitHub - 1 maintainer
mnem 1.24.0
Mixture Nested Effects Models5 versions - Latest release: 5 months ago - 4 dependent packages - 13.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
SMITE 1.36.0
Significance-based Modules Integrating the Transcriptome and Epigenome5 versions - Latest release: 4 months ago - 16.5 thousand downloads total - 1 stars on GitHub - 2 maintainers
dcanr 1.24.0
Differential co-expression/association network analysis5 versions - Latest release: 5 months ago - 1 dependent package - 14.8 thousand downloads total - 6 stars on GitHub - 1 maintainer
netDx 1.20.0
Network-based patient classifier5 versions - Latest release: 4 months ago - 6.26 thousand downloads total - 1 maintainer
BiRewire 3.40.0
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), u...5 versions - Latest release: 4 months ago - 34.6 thousand downloads total - 1 maintainer
epiNEM 1.32.0
epiNEM5 versions - Latest release: 5 months ago - 4 dependent packages - 17.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
ternarynet 1.52.0
Ternary Network Estimation5 versions - Latest release: 4 months ago - 23.9 thousand downloads total - 1 maintainer
CNORfuzzy 1.50.0
Addon to CellNOptR: Fuzzy Logic5 versions - Latest release: 4 months ago - 26.5 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
6 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
EGSEA 1.36.0
Ensemble of Gene Set Enrichment Analyses6 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
SingleCellSignalR 1.20.0
Cell Signalling Using Single Cell RNAseq Data Analysis5 versions - Latest release: 4 months ago - 3 dependent packages - 19.3 thousand downloads total - 1 maintainer
netresponse 1.68.0
Functional Network Analysis5 versions - Latest release: 5 months ago - 30.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
BioNAR 1.10.0
Biological Network Analysis in R10 versions - Latest release: 4 months ago - 6.2 thousand downloads total - 1 maintainer
ADImpute 1.18.0
Adaptive Dropout Imputer (ADImpute)5 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
CBNplot 1.8.0
plot bayesian network inferred from gene expression data based on enrichment analysis results7 versions - Latest release: 4 months ago - 7.35 thousand downloads total - 56 stars on GitHub - 1 maintainer
vtpnet 0.48.0
variant-transcription factor-phenotype networks5 versions - Latest release: 4 months ago - 22.8 thousand downloads total - 1 maintainer
Pigengene 1.34.0
Infers biological signatures from gene expression data5 versions - Latest release: 4 months ago - 1 dependent package - 19.4 thousand downloads total - 1 maintainer
GmicR 1.22.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...5 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 1 maintainer
R3CPET 1.40.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process6 versions - Latest release: 4 months ago - 17.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
cliqueMS 1.22.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data6 versions - Latest release: 4 months ago - 12 thousand downloads total - 1 maintainer
rTRM 1.46.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks5 versions - Latest release: 5 months ago - 1 dependent package - 26 thousand downloads total - 3 stars on GitHub - 1 maintainer
Informeasure 1.18.0
R implementation of information measures6 versions - Latest release: 5 months ago - 7.19 thousand downloads total - 3 stars on GitHub - 1 maintainer
fgga 1.16.0
Hierarchical ensemble method based on factor graph6 versions - Latest release: 5 months ago - 7.42 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 74.1 thousand downloads total - 1 maintainer
BioNet 1.68.0
Routines for the functional analysis of biological networks5 versions - Latest release: 4 months ago - 3 dependent packages - 74.1 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
5 versions - Latest release: 4 months ago - 3 dependent packages - 36 thousand downloads total - 1 maintainer
RTN 2.32.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons5 versions - Latest release: 4 months ago - 3 dependent packages - 36 thousand downloads total - 1 maintainer
PPInfer 1.34.0
Inferring functionally related proteins using protein interaction networks5 versions - Latest release: 4 months ago - 1 dependent package - 18 thousand downloads total - 1 maintainer
iNETgrate 1.6.0
Integrates DNA methylation data with gene expression in a single gene network4 versions - Latest release: 4 months ago - 4.77 thousand downloads total - 65 stars on GitHub - 1 maintainer
MetNet 1.26.1
Inferring metabolic networks from untargeted high-resolution mass spectrometry data6 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 1 maintainer
DeMAND 1.38.0
DeMAND5 versions - Latest release: 4 months ago - 16.1 thousand downloads total - 2 maintainers
BayesKnockdown 1.34.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data5 versions - Latest release: 4 months ago - 16 thousand downloads total - 1 maintainer
MetaboSignal 1.38.0
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways6 versions - Latest release: 4 months ago - 19.4 thousand downloads total - 2 maintainers
Top 8.9% on bioconductor.org
5 versions - Latest release: 4 months ago - 6 dependent packages - 44.1 thousand downloads total - 1 maintainer
CellNOptR 1.54.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...5 versions - Latest release: 4 months ago - 6 dependent packages - 44.1 thousand downloads total - 1 maintainer
TreeAndLeaf 1.20.0
Displaying binary trees with focus on dendrogram leaves5 versions - Latest release: 4 months ago - 1 dependent package - 12.5 thousand downloads total - 1 maintainer
rTRMui 1.46.0
A shiny user interface for rTRM5 versions - Latest release: 4 months ago - 21.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
transcriptogramer 1.30.0
Transcriptional analysis based on transcriptograms5 versions - Latest release: 5 months ago - 13.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
MOGAMUN 1.18.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks5 versions - Latest release: 4 months ago - 7.81 thousand downloads total - 12 stars on GitHub - 1 maintainer
paxtoolsr 1.42.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons5 versions - Latest release: 4 months ago - 27.5 thousand downloads total - 10 stars on GitHub - 1 maintainer
netSmooth 1.28.0
Network smoothing for scRNAseq5 versions - Latest release: 4 months ago - 1 dependent package - 13.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
MoonlightR 1.34.0
Identify oncogenes and tumor suppressor genes from omics data5 versions - Latest release: 4 months ago - 16.9 thousand downloads total - 17 stars on GitHub - 1 maintainer
TRONCO 2.40.0
TRONCO, an R package for TRanslational ONCOlogy5 versions - Latest release: 4 months ago - 22 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
5 versions - Latest release: 4 months ago - 9 dependent packages - 140 thousand downloads total - 1 maintainer
minet 3.66.0
Mutual Information NETworks5 versions - Latest release: 4 months ago - 9 dependent packages - 140 thousand downloads total - 1 maintainer
Path2PPI 1.38.0
Prediction of pathway-related protein-protein interaction networks5 versions - Latest release: 4 months ago - 17.9 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
7 versions - Latest release: 4 months ago - 14 dependent packages - 1.63 million downloads total - 1 maintainer
GOSemSim 2.34.0
GO-terms Semantic Similarity Measures7 versions - Latest release: 4 months ago - 14 dependent packages - 1.63 million downloads total - 1 maintainer
PIUMA 1.4.0
Phenotypes Identification Using Mapper from topological data Analysis3 versions - Latest release: 4 months ago - 3.66 thousand downloads total - 5 stars on GitHub - 1 maintainer
dce 1.13.0
Pathway Enrichment Based on Differential Causal Effects4 versions - Latest release: 10 months ago - 6.67 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
5 versions - Latest release: 4 months ago - 1 dependent package - 32.6 thousand downloads total - 1 maintainer
FGNet 3.42.0
Functional Gene Networks derived from biological enrichment analyses5 versions - Latest release: 4 months ago - 1 dependent package - 32.6 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
5 versions - Latest release: 4 months ago - 35.1 thousand downloads total - 1 maintainer
SBMLR 2.4.0
SBML-R Interface and Analysis Tools5 versions - Latest release: 4 months ago - 35.1 thousand downloads total - 1 maintainer
levi 1.26.0
Landscape Expression Visualization Interface5 versions - Latest release: 4 months ago - 9.44 thousand downloads total - 1 maintainer
Related Keywords
Software
185
GraphAndNetwork
90
GeneExpression
79
Pathways
60
NetworkInference
51
SystemsBiology
45
NetworkEnrichment
43
DifferentialExpression
39
Clustering
29
GeneRegulation
27
RNASeq
27
GeneSetEnrichment
27
Visualization
26
Microarray
24
Transcriptomics
22
ImmunoOncology
22
KEGG
22
Transcription
20
Sequencing
18
StatisticalMethod
17
Classification
17
Proteomics
16
SingleCell
15
Metabolomics
14
GeneTarget
14
Regression
13
GO
12
bioinformatics
12
Reactome
11
DataImport
11
BiomedicalInformatics
11
Genetics
10
FunctionalGenomics
10
Bayesian
10
DataRepresentation
9
Normalization
9
CellBiology
8
DimensionReduction
8
QualityControl
8
DifferentialMethylation
8
DNAMethylation
8
r
8
Annotation
7
GenePrediction
7
Survival
7
Preprocessing
7
mRNAMicroarray
7
bioconductor
6
MethylationArray
6
TimeCourse
6
ThirdPartyClient
6
GUI
6
GeneSignaling
6
NeuralNetwork
5
GenomeWideAssociation
5
Infrastructure
5
MultipleComparison
5
rstats
5
SNP
4
r-package
4
Coverage
4
FunctionalPrediction
4
miRNA
4
DNASeq
4
ATACSeq
4
pathways
4
TwoChannel
4
network
3
Epigenetics
3
BatchEffect
3
FeatureExtraction
3
GeneticVariability
3
genomics
3
bioconductor-package
3
DecisionTree
3
CopyNumberVariation
3
PrincipalComponent
3
CellBasedAssays
3
MassSpectrometry
3
ComparativeGenomics
3
Phylogenetics
3
networks
3
comparative-genomics
3
evolutionary-genomics
2
tcga
2
visualization
2
pathway-enrichment-analysis
2
SequenceMatching
2
ShinyApps
2
ChIPSeq
2
VariantAnnotation
2
network-analysis
2
gene
2
AnnotationData
2
systems-biology
2
bioconductor-packages
2
PooledScreens
2
CRISPR
2
transcriptomics
2
pathway-analysis
2