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bioconductor.org "DNAMethylation" keyword

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

DAMEfinder 1.20.0
Finds DAMEs - Differential Allelicly MEthylated regions
5 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.60.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
5 versions - Latest release: 3 months ago - 10 dependent packages - 365 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
missMethyl 1.42.0
Analysing Illumina HumanMethylation BeadChip Data
6 versions - Latest release: 3 months ago - 5 dependent packages - 151 thousand downloads total - 4 maintainers
Top 1.9% on bioconductor.org
minfi 1.54.1
Analyze Illumina Infinium DNA methylation arrays
7 versions - Latest release: 3 months ago - 31 dependent packages - 850 thousand downloads total - 60 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R
23 versions - Latest release: 16 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
methrix 1.22.1
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
6 versions - Latest release: about 2 months ago - 1 dependent package - 11.4 thousand downloads total - 32 stars on GitHub - 1 maintainer
planet 1.16.0
Placental DNA methylation analysis tools
5 versions - Latest release: 3 months ago - 1 dependent package - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.4.0
Methylation array and sequencing spatial analysis methods
12 versions - Latest release: 3 months ago - 2 dependent packages - 166 thousand downloads total - 1 maintainer
deconvR 1.14.0
Simulation and Deconvolution of Omic Profiles
5 versions - Latest release: 3 months ago - 8.85 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 10.0% on bioconductor.org
EpiDISH 2.24.0
Epigenetic Dissection of Intra-Sample-Heterogeneity
5 versions - Latest release: 2 months ago - 2 dependent packages - 43.7 thousand downloads total - 50 stars on GitHub - 1 maintainer
methodical 1.4.0
Discovering genomic regions where methylation is strongly associated with transcriptional activity
4 versions - Latest release: 3 months ago - 3.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.36.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
7 versions - Latest release: 2 months ago - 7 dependent packages - 474 thousand downloads total - 321 stars on GitHub - 2 maintainers
betaHMM 1.4.1
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...
4 versions - Latest release: 2 months ago - 3.39 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
sesame 1.26.0
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
7 versions - Latest release: 3 months ago - 4 dependent packages - 71.1 thousand downloads total - 72 stars on GitHub - 1 maintainer
EnMCB 1.20.0
Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
5 versions - Latest release: 3 months ago - 8.98 thousand downloads total - 9 stars on GitHub - 1 maintainer
NanoMethViz 3.4.0
Visualise methylation data from Oxford Nanopore sequencing
5 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
MEAT 1.20.0
Muscle Epigenetic Age Test
5 versions - Latest release: 2 months ago - 8.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
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
MBAmethyl 1.42.0
Model-based analysis of DNA methylation data
5 versions - Latest release: 3 months ago - 16.3 thousand downloads total - 1 maintainer
knowYourCG 1.4.0
Functional analysis of DNA methylome datasets
5 versions - Latest release: 2 months ago - 3.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
Repitools 1.54.0
Epigenomic tools
5 versions - Latest release: 3 months ago - 1 dependent package - 79.7 thousand downloads total - 1 maintainer
TOAST 1.22.0
Tools for the analysis of heterogeneous tissues
5 versions - Latest release: 3 months ago - 3 dependent packages - 28.4 thousand downloads total - 8 stars on GitHub - 1 maintainer
BEAT 1.46.0
BEAT - BS-Seq Epimutation Analysis Toolkit
5 versions - Latest release: 3 months ago - 22.2 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
bumphunter 1.50.0
Bump Hunter
5 versions - Latest release: 3 months ago - 15 dependent packages - 460 thousand downloads total - 15 stars on GitHub - 1 maintainer
bigmelon 1.34.0
Illumina methylation array analysis for large experiments
5 versions - Latest release: 3 months ago - 18.7 thousand downloads total - 1 maintainer
TENET 1.0.1
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key...
2 versions - Latest release: about 2 months ago - 937 downloads total - 1 stars on GitHub - 1 maintainer
conumee 1.42.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
5 versions - Latest release: 3 months ago - 30.4 thousand downloads total - 1 maintainer
methylclock 1.14.0
Methylclock - DNA methylation-based clocks
5 versions - Latest release: 3 months ago - 13 thousand downloads total - 40 stars on GitHub - 1 maintainer
MethylAid 1.42.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets
5 versions - Latest release: 3 months ago - 25.3 thousand downloads total - 1 maintainer
spiky 1.14.0
Spike-in calibration for cell-free MeDIP
5 versions - Latest release: 2 months ago - 6.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
methimpute 1.30.0
Imputation-guided re-construction of complete methylomes from WGBS data
5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 1 maintainer
methylCC 1.22.0
Estimate the cell composition of whole blood in DNA methylation samples
5 versions - Latest release: 3 months ago - 10.7 thousand downloads total - 19 stars on GitHub - 1 maintainer
MEAL 1.38.0
Perform methylation analysis
5 versions - Latest release: 3 months ago - 19.7 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
MethylSeekR 1.48.0
Segmentation of Bis-seq data
5 versions - Latest release: 3 months ago - 2 dependent packages - 36.6 thousand downloads total - 1 maintainer
Top 6.6% on bioconductor.org
methylumi 2.54.0
Handle Illumina methylation data
5 versions - Latest release: 3 months ago - 7 dependent packages - 332 thousand downloads total - 8 stars on GitHub - 1 maintainer
skewr 1.40.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
5 versions - Latest release: 3 months ago - 16 thousand downloads total - 1 maintainer
vmrseq 1.0.1
Probabilistic Modeling of Single-cell Methylation Heterogeneity
2 versions - Latest release: about 2 months ago - 597 downloads total - 9 stars on GitHub - 1 maintainer
methylscaper 1.16.0
Visualization of Methylation Data
6 versions - Latest release: 3 months ago - 6.75 thousand downloads total - 1 stars on GitHub - 1 maintainer
ramr 1.16.0
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
5 versions - Latest release: 3 months ago - 7.14 thousand downloads total - 0 stars on GitHub - 1 maintainer
epialleleR 1.16.0
Fast, Epiallele-Aware Methylation Caller and Reporter
5 versions - Latest release: 3 months ago - 7.22 thousand downloads total - 6 stars on GitHub - 1 maintainer
TransView 1.52.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
6 versions - Latest release: 3 months ago - 25.4 thousand downloads total - 1 maintainer
EpiMix 1.10.0
EpiMix: an integrative tool for the population-level analysis of DNA methylation
5 versions - Latest release: 3 months ago - 1 dependent package - 5.11 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.7% on bioconductor.org
bsseq 1.44.1
Analyze, manage and store whole-genome methylation data
6 versions - Latest release: about 2 months ago - 12 dependent packages - 235 thousand downloads total - 37 stars on GitHub - 1 maintainer
cbaf 1.30.0
Automated functions for comparing various omic data from cbioportal.org
6 versions - Latest release: 3 months ago - 12.9 thousand downloads total - 1 maintainer
cfTools 1.8.0
Informatics Tools for Cell-Free DNA Study
5 versions - Latest release: 2 months ago - 4.38 thousand downloads total - 6 stars on GitHub - 1 maintainer
shinyMethyl 1.44.0
Interactive visualization for Illumina methylation arrays
5 versions - Latest release: 3 months ago - 31.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
Harman 1.36.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
5 versions - Latest release: 3 months ago - 1 dependent package - 25.9 thousand downloads total - 1 maintainer
les 1.58.0
Identifying Differential Effects in Tiling Microarray Data
5 versions - Latest release: 3 months ago - 1 dependent package - 30.1 thousand downloads total - 1 maintainer
dmrseq 1.28.0
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
8 versions - Latest release: 3 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
GAprediction 1.34.0
Prediction of gestational age with Illumina HumanMethylation450 data
5 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 1 maintainer
coMethDMR 1.12.0
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide ...
5 versions - Latest release: 3 months ago - 6.08 thousand downloads total - 7 stars on GitHub - 1 maintainer
HIREewas 1.26.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
5 versions - Latest release: 3 months ago - 9.55 thousand downloads total - 1 maintainer
Melissa 1.24.0
Bayesian clustering and imputationa of single cell methylomes
5 versions - Latest release: 3 months ago - 9.22 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
MEDME 1.68.0
Modelling Experimental Data from MeDIP Enrichment
5 versions - Latest release: 3 months ago - 34.2 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.14.0
Illumina DNA methylation array normalization and metrics
5 versions - Latest release: 3 months ago - 5 dependent packages - 155 thousand downloads total - 1 maintainer
scMET 1.10.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
5 versions - Latest release: 3 months ago - 4.97 thousand downloads total - 18 stars on GitHub - 1 maintainer
regionalpcs 1.6.0
Summarizing Regional Methylation with Regional Principal Components Analysis
4 versions - Latest release: 3 months ago - 4.21 thousand downloads total - 3 stars on GitHub - 1 maintainer
methInheritSim 1.30.0
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
5 versions - Latest release: 3 months ago - 1 dependent package - 12.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
shinyepico 1.16.0
ShinyÉPICo
5 versions - Latest release: 3 months ago - 7.28 thousand downloads total - 5 stars on GitHub - 1 maintainer
omicsPrint 1.28.0
Cross omic genetic fingerprinting
5 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 1 maintainer
methylGSA 1.26.0
Gene Set Analysis Using the Outcome of Differential Methylation
5 versions - Latest release: 3 months ago - 16.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
MassArray 1.60.0
Analytical Tools for MassArray Data
5 versions - Latest release: 3 months ago - 30.1 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
BiSeq 1.48.1
Processing and analyzing bisulfite sequencing data
6 versions - Latest release: about 2 months ago - 40.8 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.26.0
RnBeads
5 versions - Latest release: 3 months ago - 1 dependent package - 65.6 thousand downloads total - 1 maintainer
epimutacions 1.12.0
Robust outlier identification for DNA methylation data
6 versions - Latest release: 3 months ago - 5.79 thousand downloads total - 0 stars on GitHub - 1 maintainer
borealis 1.12.0
Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution
5 versions - Latest release: 3 months ago - 5.25 thousand downloads total - 1 maintainer
funtooNorm 1.32.0
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
5 versions - Latest release: 3 months ago - 12.9 thousand downloads total - 1 maintainer
GEM 1.34.0
GEM: fast association study for the interplay of Gene, Environment and Methylation
5 versions - Latest release: 3 months ago - 13.7 thousand downloads total - 1 maintainer
MethylMix 2.38.0
MethylMix: Identifying methylation driven cancer genes
5 versions - Latest release: 3 months ago - 27.2 thousand downloads total - 1 maintainer
TurboNorm 1.56.0
A fast scatterplot smoother suitable for microarray normalization
5 versions - Latest release: 3 months ago - 27.7 thousand downloads total - 1 maintainer
MoonlightR 1.34.0
Identify oncogenes and tumor suppressor genes from omics data
5 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
ramwas 1.32.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
mitch 1.20.0
Multi-Contrast Gene Set Enrichment Analysis
7 versions - Latest release: 3 months ago - 8.59 thousand downloads total - 16 stars on GitHub - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA
5 versions - Latest release: 3 months ago - 6.23 thousand downloads total - 26 stars on GitHub - 1 maintainer
ENmix 1.44.1
Quality control and analysis tools for Illumina DNA methylation BeadChip
8 versions - Latest release: about 2 months ago - 37.6 thousand downloads total - 1 maintainer
SingleMoleculeFootprinting 2.2.0
Analysis tools for Single Molecule Footprinting (SMF) data
5 versions - Latest release: 3 months ago - 6.51 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
HELP 1.66.0
Tools for HELP data analysis
5 versions - Latest release: 3 months ago - 34.1 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
RTCGA 1.38.0
The Cancer Genome Atlas Data Integration
5 versions - Latest release: 3 months ago - 1 dependent package - 82.6 thousand downloads total - 51 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
MEDIPS 1.60.0
DNA IP-seq data analysis
5 versions - Latest release: 3 months ago - 54.5 thousand downloads total - 1 maintainer
normalize450K 1.36.0
Preprocessing of Illumina Infinium 450K data
5 versions - Latest release: 3 months ago - 13.5 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
ELMER 2.32.0
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
5 versions - Latest release: 3 months ago - 44.3 thousand downloads total - 1 maintainer
MethPed 1.36.0
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
5 versions - Latest release: 3 months ago - 14.5 thousand downloads total - 1 maintainer
methylMnM 1.46.0
detect different methylation level (DMR)
5 versions - Latest release: 3 months ago - 1 dependent package - 22.2 thousand downloads total
DMRcaller 1.40.0
Differentially Methylated Regions caller
5 versions - Latest release: 3 months ago - 22.9 thousand downloads total - 1 maintainer
MPFE 1.44.0
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
5 versions - Latest release: 3 months ago - 15.9 thousand downloads total - 1 maintainer
PoDCall 1.16.0
Positive Droplet Calling for DNA Methylation Droplet Digital PCR
6 versions - Latest release: 3 months ago - 5.63 thousand downloads total - 1 maintainer
methylSig 1.20.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
5 versions - Latest release: 3 months ago - 9.19 thousand downloads total - 15 stars on GitHub - 1 maintainer
ARRmNormalization 1.48.0
Adaptive Robust Regression normalization for Illumina methylation data
5 versions - Latest release: 3 months ago - 27.3 thousand downloads total - 1 maintainer
recountmethylation 1.18.0
Access and analyze public DNA methylation array data compilations
5 versions - Latest release: 3 months ago - 8.05 thousand downloads total - 8 stars on GitHub - 1 maintainer
methyLImp2 1.4.0
Missing value estimation of DNA methylation data
3 versions - Latest release: 3 months ago - 3.43 thousand downloads total - 4 stars on GitHub - 1 maintainer
Moonlight2R 1.6.0
Identify oncogenes and tumor suppressor genes from omics data
4 versions - Latest release: 3 months ago - 4.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
CTexploreR 1.4.0
Explores Cancer Testis Genes
3 versions - Latest release: 3 months ago - 3.25 thousand downloads total - 0 stars on GitHub - 1 maintainer
COCOA 2.22.0
Coordinate Covariation Analysis
5 versions - Latest release: 3 months ago - 11.2 thousand downloads total - 1 maintainer
qsea 1.34.0
IP-seq data analysis and vizualization
5 versions - Latest release: 3 months ago - 15.4 thousand downloads total - 1 maintainer
MIRA 1.30.0
Methylation-Based Inference of Regulatory Activity
5 versions - Latest release: 3 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
methylPipe 1.42.1
Base resolution DNA methylation data analysis
6 versions - Latest release: about 2 months ago - 1 dependent package - 26 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
DSS 2.56.0
Dispersion shrinkage for sequencing data
6 versions - Latest release: 3 months ago - 10 dependent packages - 165 thousand downloads total - 2 maintainers
mCSEA 1.28.0
Methylated CpGs Set Enrichment Analysis
6 versions - Latest release: 3 months ago - 1 dependent package - 14.2 thousand downloads total - 1 maintainer
iNETgrate 1.6.0
Integrates DNA methylation data with gene expression in a single gene network
4 versions - Latest release: 3 months ago - 4.25 thousand downloads total - 65 stars on GitHub - 1 maintainer
iCheck 1.38.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
5 versions - Latest release: 3 months ago - 16.7 thousand downloads total - 1 maintainer
Related Keywords
Software 122 Epigenetics 49 DifferentialMethylation 48 MethylationArray 42 Sequencing 41 Microarray 39 Preprocessing 34 GeneExpression 29 ImmunoOncology 29 MethylSeq 26 QualityControl 26 TwoChannel 20 Normalization 18 DifferentialExpression 17 DataImport 16 Coverage 16 Regression 15 Genetics 15 GeneRegulation 14 CpGIsland 13 Visualization 13 Transcription 11 SingleCell 11 RNASeq 11 StatisticalMethod 10 MultipleComparison 10 Transcriptomics 9 BiomedicalInformatics 9 Network 8 CopyNumberVariation 8 BatchEffect 8 Clustering 8 GeneSetEnrichment 7 Survival 7 WholeGenome 7 PrincipalComponent 7 dna-methylation 7 ChIPSeq 7 Pathways 7 FunctionalGenomics 7 SystemsBiology 6 methylation 6 Bayesian 6 GenomeWideAssociation 6 SNP 6 GenomeAnnotation 6 bioconductor 5 OneChannel 5 FeatureExtraction 5 BiologicalQuestion 4 GeneTarget 4 Classification 4 GeneticVariability 4 HiddenMarkovModel 3 KEGG 3 bioconductor-package 3 DataRepresentation 3 r 3 bioinformatics 3 MultiChannel 3 GenomicVariation 3 Proteomics 3 CellBiology 3 GraphAndNetwork 2 mRNAMicroarray 2 LongRead 2 GUI 2 r-package 2 NucleosomePositioning 2 GenePrediction 2 DimensionReduction 2 next-generation-sequencing 2 NetworkEnrichment 2 MotifAnnotation 2 ATACSeq 2 inheritance 2 Spatial 2 TimeCourse 2 Annotation 2 ExperimentHubSoftware 1 missing-value-imputation 1 imputation 1 latent-factor-model 1 ExperimentHub 1 missing-data 1 missing-values 1 differential-methylation 1 ddPCR 1 HighThroughputSequencingData 1 rpackage 1 stochastic-gradient-descent 1 SequenceMatching 1 single-cell-methylation 1 ReportWriting 1 pathway-analysis 1 gene-seq-analysis 1 gene-regulation 1 Reactome 1 TissueMicroarray 1 dimensionality-reduction 1