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.
Bioconductor version: Release (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 (from within R,
enter citation("M3D")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("M3D")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("M3D")
R Script | An Introduction to the M$^3$D method | |
Reference Manual | ||
Text | NEWS |
biocViews | Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software |
Version | 1.22.0 |
In Bioconductor since | BioC 3.0 (R-3.1) (6 years) |
License | Artistic License 2.0 |
Depends | R (>= 3.3.0) |
Imports | parallel, Rcpp, BiocGenerics, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, BiSeq |
LinkingTo | Rcpp |
Suggests | BiocStyle, knitr, testthat |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
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 |
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