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MethylMix

This is the development version of MethylMix; for the stable release version, see MethylMix.

MethylMix: Identifying methylation driven cancer genes


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, GeneRegulation, MethylationArray, Network, Pathways, Software, StatisticalMethod
Version 2.33.0
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
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Suggests BiocStyle, doParallel, testthat, knitr, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MethylMix_2.33.0.tar.gz
Windows Binary MethylMix_2.33.0.zip
macOS Binary (x86_64) MethylMix_2.33.0.tgz
macOS Binary (arm64)
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/
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