https://github.com/kdkorthauer/dmrseq
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
https://github.com/kdkorthauer/dmrseq
bioconductor bisulfite-sequencing dmr epigenetics inference methylation
Last synced: 4 months ago
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R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
- Host: GitHub
- URL: https://github.com/kdkorthauer/dmrseq
- Owner: kdkorthauer
- License: mit
- Created: 2017-07-14T22:48:24.000Z (almost 9 years ago)
- Default Branch: devel
- Last Pushed: 2025-05-09T17:38:40.000Z (about 1 year ago)
- Last Synced: 2025-05-09T18:35:20.871Z (about 1 year ago)
- Topics: bioconductor, bisulfite-sequencing, dmr, epigenetics, inference, methylation
- Language: R
- Homepage:
- Size: 22.9 MB
- Stars: 58
- Watchers: 9
- Forks: 14
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](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.