dmrseq: Inference for differentially methylated regions (DMRs) from bisulfite sequencing

A central question in the analysis of bisulfite sequencing data
is to detect regions (collections of
neighboring CpGs) with systematic differences between conditions,
as compared to within-condition variability. These so-called Differentially
Methylated Regions (DMRs) are thought to be more informative than single CpGs
in terms of of biological function.

The package dmrseq
provides a rigorous permutation-based approach to
detect and perform inference for differential methylation by use of
generalized least squares models that account for inter-individual and
inter-CpG variability to generate region-level statistics that can be
comparable across the genome. The framework performs well even
on samples as small as two per group.

Installation

dmrseq is available on
Bioconductor. You can install
it with R version 3.5.0 or higher with the following commands:

install.packages("BiocManager")
BiocManager::install("dmrseq")

Getting started

See the vignette for information on how to use the package to perform
typical methylation analysis workflows.

Learn more

More details of the dmrseq framework can be found in the manuscript

Korthauer, K., Chakraborty, S., Benjamini, Y., and Irizarry, R.A.
Detection and accurate False Discovery Rate control of differentially
methylated regions from Whole Genome Bisulfite Sequencing
Biostatistics, 2018 (in press).
BioRxiv:10.1101/183210