Package: MethylMix
Title: MethylMix: Identifying methylation driven cancer genes
Version: 2.41.0
Description: 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.
Depends: R (>= 3.2.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
Author: Olivier Gevaert
Maintainer: Olivier Gevaert <olivier.gevaert@gmail.com>
Type: Package
Date: 2018-07-13
Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
        data.table, limma, R.matlab, digest
Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown
biocViews:
        DNAMethylation,StatisticalMethod,DifferentialMethylation,GeneRegulation,GeneExpression,MethylationArray,DifferentialExpression,Pathways,Network
RoxygenNote: 6.0.1
VignetteBuilder: knitr
Config/pak/sysreqs: make
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:21:12 UTC
RemoteUrl: https://github.com/bioc/MethylMix
RemoteRef: HEAD
RemoteSha: 4e0a470cc528103504a17a13cb310c82637acad9
NeedsCompilation: no
Packaged: 2026-02-21 07:16:58 UTC; root
Built: R 4.6.0; ; 2026-02-21 07:18:23 UTC; windows
