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dmrseq

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


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("dmrseq")

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

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 PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome
Version 1.22.1
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
System Requirements
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Suggests knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package dmrseq_1.22.1.tar.gz
Windows Binary dmrseq_1.22.1.zip
macOS Binary (x86_64) dmrseq_1.22.1.tgz
macOS Binary (arm64) dmrseq_1.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/dmrseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/dmrseq
Bioc Package Browser https://code.bioconductor.org/browse/dmrseq/
Package Short Url https://bioconductor.org/packages/dmrseq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive