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DMRforPairs

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.18 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: Release (3.18)

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 (version "4.3") 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

Reference Manual PDF

Details

biocViews Annotation, DNAMethylation, DifferentialMethylation, Microarray, ReportWriting, Software, Visualization
Version 1.38.0
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/
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
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Source Repository git clone https://git.bioconductor.org/packages/DMRforPairs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DMRforPairs
Package Short Url https://bioconductor.org/packages/DMRforPairs/
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