# 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.
<img src="/inst/sticker/dmrseq.png" height="300"/>
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.
**dmrseq** is available on
[Bioconductor](https://bioconductor.org/packages/dmrseq). You can install
it with R version 3.5.0 or higher with the following commands:
## 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).
This package is made available under an MIT license.