# 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. <p align="center"> <img src="/inst/sticker/dmrseq.png" height="300"/> </p> 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](https://bioconductor.org/packages/dmrseq). 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](http://www.biorxiv.org/content/early/2017/08/31/183210) ## License/Copyright [](https://opensource.org/licenses/MIT) This package is made available under an MIT license.