DMRforPairs
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DMRforPairs.
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
Bioconductor version: 3.9
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("DMRforPairs")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DMRforPairs")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DMRforPairs")| DMRforPairs_vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DNAMethylation, DifferentialMethylation, Microarray, ReportWriting, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.2), Gviz(>= 1.2.1), R2HTML (>= 2.2.1), GenomicRanges(>= 1.10.7), parallel |
| Imports | |
| System Requirements | |
| URL | http://www.martinrijlaarsdam.nl http://www.erasmusmc.nl/pathologie/research/lepo/3898639/ |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DMRforPairs_1.20.0.tar.gz |
| Windows Binary | DMRforPairs_1.20.0.zip |
| Mac OS X 10.11 (El Capitan) | DMRforPairs_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DMRforPairs |
| Source Repository (Developer Access) | git clone [email protected]:packages/DMRforPairs |
| Bioc Package Browser | https://code.bioconductor.org/browse/DMRforPairs/ |
| Package Short Url | https://bioconductor.org/packages/DMRforPairs/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |