bioconductor.org "Network" keyword
Top 2.7% on bioconductor.org
9 versions - Latest release: 6 months ago - 7 dependent packages - 664 thousand downloads total - 354 stars on GitHub - 2 maintainers
TCGAbiolinks 2.40.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data9 versions - Latest release: 6 months ago - 7 dependent packages - 664 thousand downloads total - 354 stars on GitHub - 2 maintainers
Top 1.4% on bioconductor.org
7 versions - Latest release: 6 months ago - 33 dependent packages - 2.06 million downloads total - 1 maintainer
RBGL 1.88.0
An interface to the BOOST graph library7 versions - Latest release: 6 months ago - 33 dependent packages - 2.06 million downloads total - 1 maintainer
IMMAN 1.32.0
Interlog protein network reconstruction by Mapping and Mining ANalysis7 versions - Latest release: 5 months ago - 23.8 thousand downloads total - 1 maintainer
rWikiPathways 1.32.0
rWikiPathways - R client library for the WikiPathways API7 versions - Latest release: 6 months ago - 5 dependent packages - 93.4 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
7 versions - Latest release: 5 months ago - 46.6 thousand downloads total - 1 maintainer
GraphAlignment 1.76.0
GraphAlignment7 versions - Latest release: 5 months ago - 46.6 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
7 versions - Latest release: 5 months ago - 3 dependent packages - 106 thousand downloads total - 1 maintainer
BioNet 1.72.0
Routines for the functional analysis of biological networks7 versions - Latest release: 5 months ago - 3 dependent packages - 106 thousand downloads total - 1 maintainer
cosmosR 1.20.0
COSMOS (Causal Oriented Search of Multi-Omic Space)8 versions - Latest release: 5 months ago - 23.5 thousand downloads total - 70 stars on GitHub - 1 maintainer
CARNIVAL 2.22.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...7 versions - Latest release: 6 months ago - 2 dependent packages - 32.4 thousand downloads total - 62 stars on GitHub - 1 maintainer
decoupleR 2.17.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data8 versions - Latest release: 6 months ago - 3 dependent packages - 129 thousand downloads total - 311 stars on GitHub - 1 maintainer
GWENA 1.22.0
Pipeline for augmented co-expression analysis7 versions - Latest release: 6 months ago - 31.4 thousand downloads total - 18 stars on GitHub - 1 maintainer
MetNet 1.30.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data9 versions - Latest release: 6 months ago - 32.4 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
8 versions - Latest release: 6 months ago - 3 dependent packages - 58 thousand downloads total - 1 maintainer
RTN 2.36.0
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons8 versions - Latest release: 6 months ago - 3 dependent packages - 58 thousand downloads total - 1 maintainer
MethylMix 2.42.0
MethylMix: Identifying methylation driven cancer genes7 versions - Latest release: 5 months ago - 48.4 thousand downloads total - 1 maintainer
KEGGlincs 1.38.0
Visualize all edges within a KEGG pathway and overlay LINCS data7 versions - Latest release: 4 months ago - 33.7 thousand downloads total - 2 maintainers
RegEnrich 1.22.1
Gene regulator enrichment analysis10 versions - Latest release: 4 months ago - 25.6 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
10 versions - Latest release: 2 months ago - 4 dependent packages - 88 thousand downloads total - 1 maintainer
RedeR 3.8.1
Interactive visualization and manipulation of nested networks10 versions - Latest release: 2 months ago - 4 dependent packages - 88 thousand downloads total - 1 maintainer
syntenet 1.14.0
Inference And Analysis Of Synteny Networks11 versions - Latest release: 5 months ago - 1 dependent package - 24.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
EGSEA 1.40.0
Ensemble of Gene Set Enrichment Analyses8 versions - Latest release: 6 months ago - 1 dependent package - 58.5 thousand downloads total - 1 maintainer
MetaboSignal 1.42.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways9 versions - Latest release: 3 months ago - 40.1 thousand downloads total - 2 maintainers
Top 9.2% on bioconductor.org
7 versions - Latest release: 5 months ago - 55.6 thousand downloads total - 1 maintainer
GraphAT 1.84.0
Graph Theoretic Association Tests7 versions - Latest release: 5 months ago - 55.6 thousand downloads total - 1 maintainer
toppgene 1.0.2
Gene List Enrichment Analysis using the ToppGene Suite3 versions - Latest release: 3 months ago - 2.06 thousand downloads total - 1 stars on GitHub - 1 maintainer
postNet 1.0.0
Post-transcriptional network modeling1 version - Latest release: 6 months ago - 4.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
annoLinker 1.0.0
Annotating genomic regions through chromatin interaction links1 version - Latest release: 6 months ago - 3.77 thousand downloads total - 0 stars on GitHub - 1 maintainer
GraphExperiment 1.0.2
S4 Class for Quantitative Data and Associated Networks2 versions - Latest release: 2 months ago - 3.64 thousand downloads total - 1 stars on GitHub - 1 maintainer
ExpoRiskR 1.0.0
Exposure-Aware Multi-Omics Risk Modeling1 version - Latest release: 6 months ago - 2.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
10 versions - Latest release: 6 days ago - 13 dependent packages - 242 thousand downloads total - 1 maintainer
STRINGdb 2.24.1
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis10 versions - Latest release: 6 days ago - 13 dependent packages - 242 thousand downloads total - 1 maintainer
BiRewire 3.44.0
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), u...8 versions - Latest release: 6 days ago - 45.8 thousand downloads total - 1 maintainer
GmicR 1.26.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...7 versions - Latest release: 5 months ago - 23.9 thousand downloads total - 1 maintainer
martini 1.32.0
GWAS Incorporating Networks7 versions - Latest release: 6 months ago - 25.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
ternarynet 1.56.0
Ternary Network Estimation7 versions - Latest release: 5 months ago - 36.2 thousand downloads total - 1 maintainer
FELLA 1.32.0
Interpretation and enrichment for metabolomics data7 versions - Latest release: 5 months ago - 1 maintainer
omicsViewer 1.16.0
Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omics...7 versions - Latest release: 6 months ago - 19.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
DeepPINCS 1.20.0
Protein Interactions and Networks with Compounds based on Sequences using Deep Learning7 versions - Latest release: 5 months ago - 2 dependent packages - 18.1 thousand downloads total - 1 maintainer
KinSwingR 1.30.0
KinSwingR: network-based kinase activity prediction7 versions - Latest release: 5 months ago - 21.7 thousand downloads total - 1 maintainer
vtpnet 0.52.0
variant-transcription factor-phenotype networks7 versions - Latest release: 6 months ago - 1 maintainer
miaSim 1.18.0
Microbiome Data Simulation7 versions - Latest release: 5 months ago - 22 stars on GitHub - 1 maintainer
dominoSignal 1.6.0
Cell Communication Analysis for Single Cell RNA Sequencing5 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 8 stars on GitHub - 1 maintainer
MSstatsBioNet 1.4.1
Network Analysis for MS-based Proteomics Experiments4 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
R3CPET 1.44.0
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process8 versions - Latest release: 5 months ago - 32.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
PathNet 1.52.0
An R package for pathway analysis using topological information7 versions - Latest release: 6 months ago - 38.4 thousand downloads total - 1 maintainer
cageminer 1.18.0
Candidate Gene Miner8 versions - Latest release: 5 months ago - 19.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
goatea 2.0.0
Interactive Exploration of GSEA by the GOAT Method3 versions - Latest release: 5 months ago - 4.24 thousand downloads total - 5 stars on GitHub - 1 maintainer
pandaR 1.44.0
PANDA Algorithm7 versions - Latest release: 5 months ago - 1 dependent package - 41.3 thousand downloads total - 2 maintainers
csdR 1.18.0
Differential gene co-expression7 versions - Latest release: 5 months ago - 15.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
GRENITS 1.64.0
Gene Regulatory Network Inference Using Time Series7 versions - Latest release: 5 months ago - 39.3 thousand downloads total - 1 maintainer
COSNet 1.46.0
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings7 versions - Latest release: 5 months ago - 31.9 thousand downloads total - 1 stars on GitHub
spatialHeatmap 2.18.2
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions18 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
drugfindR 1.0.0
Investigate iLINCS for candidate repurposable drugs1 version - Latest release: 6 months ago - 6.8 thousand downloads total - 13 stars on GitHub - 1 maintainer
miRLAB 1.42.0
Dry lab for exploring miRNA-mRNA relationships7 versions - Latest release: 6 months ago - 34.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
netprioR 1.37.0
A model for network-based prioritisation of genes7 versions - Latest release: 5 months ago - 22.9 thousand downloads total - 1 maintainer
DriverNet 1.52.0
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer7 versions - Latest release: 5 months ago - 37.5 thousand downloads total - 1 maintainer
epiregulon 2.2.0
Gene regulatory network inference from single cell epigenomic data7 versions - Latest release: 6 months ago - 1 dependent package - 14.3 thousand downloads total - 29 stars on GitHub - 1 maintainer
CCPlotR 1.10.0
Plots For Visualising Cell-Cell Interactions6 versions - Latest release: 5 months ago - 11.3 thousand downloads total - 47 stars on GitHub - 1 maintainer
TreeAndLeaf 1.24.0
Displaying binary trees with focus on dendrogram leaves8 versions - Latest release: 6 months ago - 1 dependent package - 22.6 thousand downloads total - 1 maintainer
rTRM 1.50.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks7 versions - Latest release: 5 months ago - 1 dependent package - 37.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
9 versions - Latest release: 6 months ago - 15 dependent packages - 136 thousand downloads total - 60 stars on GitHub - 1 maintainer
RCy3 2.32.0
Functions to Access and Control Cytoscape9 versions - Latest release: 6 months ago - 15 dependent packages - 136 thousand downloads total - 60 stars on GitHub - 1 maintainer
mnem 1.28.0
Mixture Nested Effects Models7 versions - Latest release: 5 months ago - 4 dependent packages - 22.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
SMITE 1.40.0
Significance-based Modules Integrating the Transcriptome and Epigenome7 versions - Latest release: 6 months ago - 26.2 thousand downloads total - 1 stars on GitHub - 2 maintainers
iModMix 1.2.0
Integrative Modules for Multi-Omics Data2 versions - Latest release: 5 months ago - 3.88 thousand downloads total - 4 stars on GitHub - 1 maintainer
DNEA 1.2.0
Differential Network Enrichment Analysis for Biological Data2 versions - Latest release: 6 months ago - 5.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
scGraphVerse 1.2.0
scGraphVerse: A Gene Network Analysis Package2 versions - Latest release: 5 months ago - 5.78 thousand downloads total - 1 stars on GitHub - 1 maintainer
netboost 2.20.0
Network Analysis Supported by Boosting8 versions - Latest release: 5 months ago - 16.5 thousand downloads total - 1 maintainer
bioCancer 1.40.0
Interactive Multi-Omics Cancers Data Visualization and Analysis9 versions - Latest release: 5 months ago - 30 thousand downloads total - 22 stars on GitHub - 1 maintainer
pathlinkR 1.8.0
Analyze and interpret RNA-Seq results6 versions - Latest release: 6 months ago - 11.2 thousand downloads total - 33 stars on GitHub - 1 maintainer
EGAD 1.40.0
Extending guilt by association by degree7 versions - Latest release: 5 months ago - 26.2 thousand downloads total - 1 maintainer
BulkSignalR 1.4.0
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spa...7 versions - Latest release: 5 months ago - 15.7 thousand downloads total - 30 stars on GitHub - 1 maintainer
PCAN 1.40.0
Phenotype Consensus ANalysis (PCAN)7 versions - Latest release: 5 months ago - 27 thousand downloads total - 1 maintainer
gatom 1.10.2
Finding an Active Metabolic Module in Atom Transition Network8 versions - Latest release: 4 months ago - 12.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
7 versions - Latest release: 5 months ago - 6 dependent packages - 57.3 thousand downloads total - 1 maintainer
CellNOptR 1.58.0
Training of boolean logic models of signalling networks using prior knowledge networks and pertur...7 versions - Latest release: 5 months ago - 6 dependent packages - 57.3 thousand downloads total - 1 maintainer
SPEM 1.52.0
S-system parameter estimation method7 versions - Latest release: 6 months ago - 1 dependent package - 31.4 thousand downloads total - 1 maintainer
ReducedExperiment 1.4.0
Containers and tools for dimensionally-reduced -omics representations4 versions - Latest release: 5 months ago - 7.65 thousand downloads total - 3 stars on GitHub - 1 maintainer
transcriptogramer 1.34.0
Transcriptional analysis based on transcriptograms7 versions - Latest release: 4 months ago - 23.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
regutools 1.24.0
regutools: an R package for data extraction from RegulonDB7 versions - Latest release: 5 months ago - 17.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
glmSparseNet 1.30.0
Network Centrality Metrics for Elastic-Net Regularized Models8 versions - Latest release: 6 months ago - 114 thousand downloads total - 6 stars on GitHub - 1 maintainer
cogeqc 1.16.0
Systematic quality checks on comparative genomics analyses9 versions - Latest release: 4 months ago - 14.3 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
7 versions - Latest release: 5 months ago - 54.2 thousand downloads total - 1 maintainer
pathifier 1.50.0
Quantify deregulation of pathways in cancer7 versions - Latest release: 5 months ago - 54.2 thousand downloads total - 1 maintainer
epiNEM 1.36.0
epiNEM7 versions - Latest release: 5 months ago - 4 dependent packages - 25.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
MOGAMUN 1.22.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks7 versions - Latest release: 5 months ago - 13.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
KBoost 1.20.0
Inference of gene regulatory networks from gene expression data7 versions - Latest release: 5 months ago - 11.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
fedup 1.19.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways7 versions - Latest release: 5 months ago - 13.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
cliqueMS 1.26.0
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data8 versions - Latest release: 6 months ago - 20.7 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
7 versions - Latest release: 5 months ago - 9 dependent packages - 178 thousand downloads total - 1 maintainer
minet 3.70.0
Mutual Information NETworks7 versions - Latest release: 5 months ago - 9 dependent packages - 178 thousand downloads total - 1 maintainer
PIUMA 1.8.0
Phenotypes Identification Using Mapper from topological data Analysis6 versions - Latest release: 5 months ago - 9.06 thousand downloads total - 5 stars on GitHub - 1 maintainer
Path2PPI 1.42.0
Prediction of pathway-related protein-protein interaction networks7 versions - Latest release: 5 months ago - 26.4 thousand downloads total - 1 maintainer
netSmooth 1.32.0
Network smoothing for scRNAseq7 versions - Latest release: 6 months ago - 1 dependent package - 22.6 thousand downloads total - 30 stars on GitHub - 1 maintainer
MoonlightR 1.38.0
Identify oncogenes and tumor suppressor genes from omics data7 versions - Latest release: 5 months ago - 26.3 thousand downloads total - 17 stars on GitHub - 1 maintainer
GSEABenchmarkeR 1.32.0
Reproducible GSEA Benchmarking8 versions - Latest release: 5 months ago - 2 dependent packages - 24.6 thousand downloads total - 14 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: almost 2 years ago - 1 dependent package - 10.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
CBNplot 1.12.0
plot bayesian network inferred from gene expression data based on enrichment analysis results9 versions - Latest release: 5 months ago - 14.7 thousand downloads total - 68 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.58.0
GRAPH Interaction from pathway Topological Environment7 versions - Latest release: 5 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
NetPathMiner 1.48.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization7 versions - Latest release: 6 months ago - 32.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
AMARETTO 1.28.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...7 versions - Latest release: 5 months ago - 24.3 thousand downloads total - 1 maintainer
mirIntegrator 1.42.0
Integrating microRNA expression into signaling pathways for pathway analysis7 versions - Latest release: 5 months ago - 26.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
7 versions - Latest release: 6 months ago - 56.6 thousand downloads total - 2 maintainers
GDCRNATools 1.32.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...7 versions - Latest release: 6 months ago - 56.6 thousand downloads total - 2 maintainers
DeMAND 1.42.0
DeMAND7 versions - Latest release: 6 months ago - 22.2 thousand downloads total - 2 maintainers
pairkat 1.18.0
PaIRKAT7 versions - Latest release: 5 months ago - 13.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
fgga 1.20.0
Hierarchical ensemble method based on factor graph8 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
RCX 1.16.0
R package implementing the Cytoscape Exchange (CX) format10 versions - Latest release: 5 months ago - 1 dependent package - 15.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
Informeasure 1.22.0
R implementation of information measures8 versions - Latest release: 5 months ago - 12.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
lionessR 1.26.0
Modeling networks for individual samples using LIONESS7 versions - Latest release: 6 months ago - 18.2 thousand downloads total - 24 stars on GitHub - 1 maintainer
Related Keywords
Software
195
GraphAndNetwork
91
GeneExpression
83
Pathways
62
NetworkInference
53
SystemsBiology
47
NetworkEnrichment
47
DifferentialExpression
42
Clustering
31
GeneSetEnrichment
31
Visualization
30
GeneRegulation
29
RNASeq
29
Transcriptomics
27
Microarray
24
KEGG
23
ImmunoOncology
22
Sequencing
20
Proteomics
20
Transcription
20
SingleCell
18
StatisticalMethod
17
Metabolomics
17
bioinformatics
16
Classification
16
Regression
14
GeneTarget
14
DataImport
13
Reactome
12
Genetics
12
GO
12
FunctionalGenomics
11
BiomedicalInformatics
11
DataRepresentation
10
Bayesian
10
Normalization
9
r
9
Annotation
9
CellBiology
8
DifferentialMethylation
8
DNAMethylation
8
DimensionReduction
8
QualityControl
8
GUI
7
ThirdPartyClient
7
mRNAMicroarray
7
bioconductor
7
Preprocessing
7
Survival
7
GenePrediction
7
GeneSignaling
6
TimeCourse
6
MethylationArray
6
rstats
6
MultipleComparison
5
FunctionalPrediction
5
NeuralNetwork
5
Infrastructure
5
GenomeWideAssociation
5
PrincipalComponent
4
transcriptomics
4
FeatureExtraction
4
pathways
4
TwoChannel
4
ATACSeq
4
DNASeq
4
r-package
4
Coverage
4
SNP
4
miRNA
4
GeneticVariability
3
CopyNumberVariation
3
BatchEffect
3
DecisionTree
3
ShinyApps
3
Epigenetics
3
bioconductor-package
3
MassSpectrometry
3
network-analysis
3
Phylogenetics
3
ComparativeGenomics
3
Microbiome
3
networks
3
comparative-genomics
3
network
3
CellBasedAssays
3
bioconductor-packages
2
SequenceMatching
2
pathway-enrichment-analysis
2
evolutionary-genomics
2
mirna
2
AnnotationData
2
SomaticMutation
2
MotifDiscovery
2
proteomics
2
ChIPSeq
2
HiC
2
tcga
2
WholeGenome
2
genomics
2