- Home
- Bioconductor 3.5
- Software Packages
- DMRforPairs
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRforPairs")
In most cases, you don't need to download the package archive at all.
DMRforPairs
|
|
|
|
|
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Bioconductor version: Release (3.5)
DMRforPairs (formerly DMR2+) allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.
Author: Martin Rijlaarsdam [aut, cre], Yvonne vd Zwan [aut], Lambert Dorssers [aut], Leendert Looijenga [aut]
Maintainer: Martin Rijlaarsdam <m.a.rijlaarsdam at gmail.com>
Citation (from within R,
enter citation("DMRforPairs")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DMRforPairs")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DMRforPairs")
| R Script | DMRforPairs_vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, DNAMethylation, DifferentialMethylation, Microarray, ReportWriting, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (3.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.2), Gviz(>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges(>= 1.10.7), parallel |
| Imports | |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | http://www.martinrijlaarsdam.nl http://www.erasmusmc.nl/pathologie/research/lepo/3898639/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DMRforPairs_1.12.0.tar.gz |
| Windows Binary | DMRforPairs_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | DMRforPairs_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMRforPairs |
| Package Short Url | http://bioconductor.org/packages/DMRforPairs/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
