To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("M3D")
In most cases, you don't need to download the package archive at all.
M3D
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Identifies differentially methylated regions across testing groups
Bioconductor version: Release (3.5)
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("M3D")
Documentation
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 |
Details
| biocViews | Coverage, CpGIsland, DNAMethylation, DifferentialMethylation, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (3 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | M3D_1.10.0.tar.gz |
| Windows Binary | M3D_1.10.0.zip (64-bit only) |
| Mac OS X 10.11 (El Capitan) | M3D_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/M3D |
| Package Short Url | http://bioconductor.org/packages/M3D/ |
| Package Downloads Report | Download Stats |
Documentation »
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