bioconductor.org "Network" keyword
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: 5 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
rWikiPathways 1.32.0
rWikiPathways - R client library for the WikiPathways API7 versions - Latest release: 5 months ago - 5 dependent packages - 91.2 thousand downloads total - 20 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: 5 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: 5 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: 4 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: 5 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: 5 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: 5 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: 5 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: 4 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: 5 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: 5 months ago - 5.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
annoLinker 1.0.0
Annotating genomic regions through chromatin interaction links1 version - Latest release: 5 months ago - 3.77 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
9 versions - Latest release: 5 months ago - 7 dependent packages - 652 thousand downloads total - 355 stars on GitHub - 2 maintainers
TCGAbiolinks 2.40.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data9 versions - Latest release: 5 months ago - 7 dependent packages - 652 thousand downloads total - 355 stars on GitHub - 2 maintainers
decoupleR 2.17.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data8 versions - Latest release: 5 months ago - 3 dependent packages - 121 thousand downloads total - 310 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: 5 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
omicsViewer 1.16.0
Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omics...7 versions - Latest release: 5 months ago - 19.5 thousand downloads total - 4 stars on GitHub - 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
Top 1.4% on bioconductor.org
7 versions - Latest release: 5 months ago - 33 dependent packages - 2.05 million downloads total - 1 maintainer
RBGL 1.88.0
An interface to the BOOST graph library7 versions - Latest release: 5 months ago - 33 dependent packages - 2.05 million downloads total - 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: 3 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: 5 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: 5 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: 4 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: 4 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: 5 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: 5 months ago - 1 dependent package - 22.6 thousand downloads total - 30 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: 5 months ago - 2 dependent packages - 29.1 thousand downloads total - 62 stars on GitHub - 1 maintainer
dominoSignal 1.6.0
Cell Communication Analysis for Single Cell RNA Sequencing5 versions - Latest release: 5 months ago - 12.4 thousand downloads total - 8 stars on GitHub - 1 maintainer
MoonlightR 1.38.0
Identify oncogenes and tumor suppressor genes from omics data7 versions - Latest release: 4 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
toppgene 1.0.2
Gene List Enrichment Analysis using the ToppGene Suite3 versions - Latest release: 2 months ago - 2.06 thousand downloads total - 1 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: 5 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: 5 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: 5 months ago - 56.6 thousand downloads total - 2 maintainers
postNet 1.0.0
Post-transcriptional network modeling1 version - Latest release: 5 months ago - 4.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
DeMAND 1.42.0
DeMAND7 versions - Latest release: 5 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: 5 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: 4 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: 5 months ago - 18.2 thousand downloads total - 24 stars on GitHub - 1 maintainer
LiquidAssociation 1.66.0
LiquidAssociation7 versions - Latest release: 5 months ago - 1 dependent package - 40.7 thousand downloads total - 1 maintainer
MIRit 1.8.0
Integrate microRNA and gene expression to decipher pathway complexity10 versions - Latest release: 5 months ago - 11.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
SingleCellSignalR 2.2.0
Cell Signalling Using Single-Cell RNA-seq or Proteomics Data7 versions - Latest release: 5 months ago - 3 dependent packages - 30.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
ExpoRiskR 1.0.0
Exposure-Aware Multi-Omics Risk Modeling1 version - Latest release: 5 months ago - 2.95 thousand downloads total - 0 stars on GitHub - 1 maintainer
tidysbml 1.6.0
Extract SBML's data into dataframes4 versions - Latest release: 5 months ago - 6.84 thousand downloads total - 2 stars on GitHub - 1 maintainer
Moonlight2R 1.10.1
Identify oncogenes and tumor suppressor genes from omics data9 versions - Latest release: 3 months ago - 12.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 37 thousand downloads total - 1 maintainer
DEGraph 1.64.0
Two-sample tests on a graph7 versions - Latest release: 5 months ago - 1 dependent package - 37 thousand downloads total - 1 maintainer
QUBIC 1.40.0
An R Package for Qualitative Biclustering in Support of Gene Co-Expression Analyses7 versions - Latest release: 3 months ago - 2 dependent packages - 39.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
rTRMui 1.50.0
A shiny user interface for rTRM7 versions - Latest release: 5 months ago - 30 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetID 1.30.0
Network-based prioritization of putative metabolite IDs7 versions - Latest release: 5 months ago - 16.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
ceRNAnetsim 1.24.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)8 versions - Latest release: 5 months ago - 13.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
vissE 1.20.0
Visualising Set Enrichment Analysis Results7 versions - Latest release: 5 months ago - 17.4 thousand downloads total - 19 stars on GitHub - 1 maintainer
netresponse 1.72.0
Functional Network Analysis7 versions - Latest release: 5 months ago - 40.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
bnem 1.20.0
Training of logical models from indirect measurements of perturbation experiments7 versions - Latest release: 5 months ago - 14.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
SGCP 1.11.1
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...10 versions - Latest release: 5 months ago - 9.65 thousand downloads total - 2 stars on GitHub - 1 maintainer
GNET2 1.27.0
Constructing gene regulatory networks from expression data through functional module inference7 versions - Latest release: 5 months ago - 15.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
epiregulon.extra 1.8.0
Companion package to epiregulon with additional plotting, differential and graph functions8 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
rScudo 1.28.0
Signature-based Clustering for Diagnostic Purposes8 versions - Latest release: 5 months ago - 17.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
RITAN 1.36.0
Rapid Integration of Term Annotation and Network resources7 versions - Latest release: 5 months ago - 21.3 thousand downloads total - 1 maintainer
HPiP 1.18.0
Host-Pathogen Interaction Prediction9 versions - Latest release: 5 months ago - 13.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
ndexr 1.34.0
NDEx R client library7 versions - Latest release: 5 months ago - 21.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
7 versions - Latest release: 5 months ago - 1 dependent package - 40.2 thousand downloads total - 1 maintainer
FGNet 3.46.0
Functional Gene Networks derived from biological enrichment analyses7 versions - Latest release: 5 months ago - 1 dependent package - 40.2 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
8 versions - Latest release: 5 months ago - 56.5 thousand downloads total - 1 maintainer
ELMER 2.35.1
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes8 versions - Latest release: 5 months ago - 56.5 thousand downloads total - 1 maintainer
dcanr 1.28.0
Differential co-expression/association network analysis7 versions - Latest release: 5 months ago - 1 dependent package - 25 thousand downloads total - 7 stars on GitHub - 1 maintainer
MODA 1.38.0
MODA: MOdule Differential Analysis for weighted gene co-expression network7 versions - Latest release: 5 months ago - 20.7 thousand downloads total - 1 maintainer
enrichViewNet 1.10.0
From functional enrichment results to biological networks8 versions - Latest release: 4 months ago - 10.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
nempi 1.20.0
Inferring unobserved perturbations from gene expression data7 versions - Latest release: 5 months ago - 13.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
Related Keywords
Software
195
GraphAndNetwork
91
GeneExpression
83
Pathways
62
NetworkInference
53
NetworkEnrichment
47
SystemsBiology
47
DifferentialExpression
42
Clustering
31
GeneSetEnrichment
31
Visualization
30
RNASeq
29
GeneRegulation
29
Transcriptomics
27
Microarray
24
KEGG
23
ImmunoOncology
22
Transcription
20
Sequencing
20
Proteomics
20
SingleCell
18
StatisticalMethod
17
Metabolomics
17
bioinformatics
16
Classification
16
GeneTarget
14
Regression
14
DataImport
13
GO
12
Genetics
12
Reactome
12
BiomedicalInformatics
11
FunctionalGenomics
11
DataRepresentation
10
Bayesian
10
Annotation
9
Normalization
9
r
9
DifferentialMethylation
8
DNAMethylation
8
QualityControl
8
CellBiology
8
DimensionReduction
8
Preprocessing
7
mRNAMicroarray
7
bioconductor
7
GUI
7
ThirdPartyClient
7
GenePrediction
7
Survival
7
MethylationArray
6
GeneSignaling
6
TimeCourse
6
rstats
6
Infrastructure
5
MultipleComparison
5
NeuralNetwork
5
GenomeWideAssociation
5
FunctionalPrediction
5
PrincipalComponent
4
pathways
4
TwoChannel
4
r-package
4
Coverage
4
miRNA
4
transcriptomics
4
DNASeq
4
ATACSeq
4
FeatureExtraction
4
SNP
4
BatchEffect
3
CopyNumberVariation
3
network-analysis
3
GeneticVariability
3
DecisionTree
3
Microbiome
3
comparative-genomics
3
ShinyApps
3
Phylogenetics
3
CellBasedAssays
3
ComparativeGenomics
3
network
3
bioconductor-package
3
MassSpectrometry
3
Epigenetics
3
networks
3
ReportWriting
2
genomics
2
bioconductor-packages
2
proteomics
2
metabolomics
2
AnnotationData
2
systems-biology
2
mirna
2
MotifDiscovery
2
HiC
2
gene
2
tcga
2
WholeGenome
2
SomaticMutation
2