dmrseq

DOI: 10.18129/B9.bioc.dmrseq    

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

Bioconductor version: Release (3.8)

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 <keegan at jimmy.harvard.edu>, Sutirtha Chakraborty <statistuta at gmail.com>, Yuval Benjamini <yuvalbenj at gmail.com>, Rafael Irizarry <rafa at jimmy.harvard.edu>

Maintainer: Keegan Korthauer <keegan at jimmy.harvard.edu>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("dmrseq", version = "3.8")

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, MultipleComparison, Regression, Sequencing, Software, WholeGenome
Version 1.2.1
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
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Enhances
URL
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Build Report  

Package Archives

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

Source Package dmrseq_1.2.1.tar.gz
Windows Binary dmrseq_1.2.1.zip
Mac OS X 10.11 (El Capitan) dmrseq_1.2.1.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 http://bioconductor.org/packages/dmrseq/
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Old Source Packages for BioC 3.8 Source Archive

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