MethylMix
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MethylMix.
MethylMix: Identifying methylation driven cancer genes
Bioconductor version: 3.7
MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert O. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8. Pierre-Louis Cedoz, Marcos Prunello, Kevin Brennan, Olivier Gevaert; MethylMix 2.0: an R package for identifying DNA methylation genes. Bioinformatics. doi:10.1093/bioinformatics/bty156.
Author: Olivier Gevaert
Maintainer: Olivier Gevaert <olivier.gevaert at gmail.com>
citation("MethylMix")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MethylMix")
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("MethylMix")| MethylMix | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, StatisticalMethod |
| Version | 2.10.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.2.0) |
| Imports | foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, doParallel, testthat, knitr, rmarkdown |
| Linking To | |
| 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 | MethylMix_2.10.2.tar.gz |
| Windows Binary | MethylMix_2.10.2.zip |
| Mac OS X 10.11 (El Capitan) | MethylMix_2.10.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MethylMix |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MethylMix |
| Bioc Package Browser | https://code.bioconductor.org/browse/MethylMix/ |
| Package Short Url | https://bioconductor.org/packages/MethylMix/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |