dmrseq

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

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DOI: 10.18129/B9.bioc.dmrseq

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0002-4565-1654 , Rafael Irizarry [aut] ORCID iD ORCID: 0000-0002-3944-4309 , 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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("dmrseq")

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