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This is the development version of dmrseq; for the stable release version, see dmrseq.

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Bioconductor version: Development (3.20)

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

Author: Keegan Korthauer [cre, aut] , Rafael Irizarry [aut] , Yuval Benjamini [aut], Sutirtha Chakraborty [aut]

Maintainer: Keegan Korthauer <keegan at>

Citation (from within R, enter citation("dmrseq")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Analyzing Bisulfite-seq data with dmrseq HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome
Version 1.25.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends R (>= 3.5), bsseq
Imports GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats(>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines
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Suggests knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
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Source Package dmrseq_1.25.0.tar.gz
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macOS Binary (x86_64) dmrseq_1.25.0.tgz
macOS Binary (arm64) dmrseq_1.25.0.tgz
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