dmrseq

DOI: 10.18129/B9.bioc.dmrseq    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DNAMethylation, DifferentialMethylation, Epigenetics, FunctionalGenomics, ImmunoOncology, MultipleComparison, Regression, Sequencing, Software, WholeGenome
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 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
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	biscuiteer
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	dmrseq_1.16.0.tar.gz
Windows Binary	dmrseq_1.16.0.zip
macOS Binary (x86_64)	dmrseq_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/dmrseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/dmrseq
Package Short Url	https://bioconductor.org/packages/dmrseq/
Package Downloads Report	Download Stats