To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("M3D")
In most cases, you don't need to download the package archive at all.
M3D
Identifies differentially methylated regions across testing groups.
Bioconductor version: 3.0
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:
source("http://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 | 1.1.4 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic License 2.0 |
| Depends | R (>= 3.0.0) |
| Imports | GenomicRanges, IRanges, BiSeq |
| LinkingTo | |
| Suggests | BiocStyle, knitr, RUnit, BiocGenerics |
| 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.
| Package Source | M3D_1.1.4.tar.gz |
| Windows Binary | M3D_1.1.4.zip |
| Mac OS X 10.6 (Snow Leopard) | M3D_1.1.4.tgz |
| Mac OS X 10.9 (Mavericks) | M3D_1.1.4.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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