M3D
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 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see M3D.
Identifies differentially methylated regions across testing groups
Bioconductor version: 3.11
This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.
Author: Tom Mayo
Maintainer: Tom Mayo <t.mayo at ed.ac.uk>
citation("M3D")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("M3D")
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("M3D")| An Introduction to the M$^3$D method | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic License 2.0 |
| Depends | R (>= 3.3.0) |
| Imports | parallel, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, testthat |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | M3D_1.22.0.tar.gz |
| Windows Binary | M3D_1.22.0.zip (64-bit only) |
| macOS 10.13 (High Sierra) | M3D_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/M3D |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/M3D |
| Package Short Url | https://bioconductor.org/packages/M3D/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |