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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylMix")
In most cases, you don't need to download the package archive at all.
MethylMix
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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MethylMix.
MethylMix: Identifying methylation driven cancer genes
Bioconductor version: 3.4
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 0. 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.
Author: Olivier Gevaert
Maintainer: Olivier Gevaert <olivier.gevaert at gmail.com>
Citation (from within R,
enter citation("MethylMix")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MethylMix")
Documentation
| HTML | R Script | MethylMix |
| Reference Manual |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, StatisticalMethod |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.2.0) |
| Imports | foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest |
| LinkingTo | |
| Suggests | BiocStyle, doParallel, testthat, knitr, rmarkdown |
| 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 | MethylMix_2.0.0.tar.gz |
| Windows Binary | MethylMix_2.0.0.zip |
| Mac OS X 10.9 (Mavericks) | MethylMix_2.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/MethylMix/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/MethylMix/ |
| Package Downloads Report | Download Stats |
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