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.

You can install dmrseq with R version 3.4.0 or higher with the following command:

devtools::install_github("kdkorthauer/dmrseq")

This assumes you have the package devtools already installed. If not, you'll first need to install it with:

install.packages("devtools")

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

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 BioRxiv 183210, 2017. 10.1101/183210

All code in this package is made available under a MIT license.
All non-code text in this project is made available under a CC BY-NC-ND 4.0 license.