Package: MethylMix
Title: MethylMix: Identifying methylation driven cancer genes
Version: 2.10.2
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 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.
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
git_url: https://git.bioconductor.org/packages/MethylMix
git_branch: RELEASE_3_7
git_last_commit: c1812cb
git_last_commit_date: 2018-07-19
Date/Publication: 2018-07-19
NeedsCompilation: no
Packaged: 2018-07-19 23:57:45 UTC; biocbuild
Built: R 3.5.1; ; 2018-07-20 07:33:44 UTC; unix
