dmrseq
This is the development version of dmrseq; for the stable release version, see dmrseq.
All Bioconductor versions of dmrseq
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Bioconductor version: 3.24 · Package version: 1.33.0
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 stat.ubc.ca>
Citation
From within R, enter citation("dmrseq"):
Keegan Korthauer, Rafael Irizarry, Yuval Benjamini, Sutirtha Chakraborty. dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing. doi:10.18129/B9.bioc.dmrseq, R package version 1.33.0, https://bioconductor.org/packages/dmrseq.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("dmrseq")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.33.0 |
| License | MIT + file LICENSE |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8 years) |
| Downloads rank | 415 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/dmrseq/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dmrseq")| Analyzing Bisulfite-seq data with dmrseq | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | dmrseq_1.33.0.tar.gz |
| Windows binary (x86_64) | dmrseq_1.33.0.zip |
| macOS binary (arm64) | dmrseq_1.33.0.tgz |
| macOS binary (x86_64) | dmrseq_1.33.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dmrseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dmrseq |
| Package Downloads Report | Download Stats |
Dependencies
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, Seqinfo, splines
Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Reverse dependencies
Imports Me (1): biscuiteer