minfi

Analyze Illumina's 450k methylation arrays

Bioconductor version: Development (3.0)

Tools for analyzing and visualizing Illumina's 450k array data

Author: Kasper Daniel Hansen [cre, aut], Martin Ayree [aut], Rafael A. Irizarry [aut], Andrew E. Jaffe [ctb], Jovana Maksimovic [ctb], E. Andres Houseman [ctb], Jean-Philippe Fortin [ctb]

Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("minfi")

Citation (from within R, enter citation("minfi")):

Documentation

PDF R Script Minfi Guide
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.11.10
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), lattice, GenomicRanges, Biostrings, utils, bumphunter(>= 1.1.9)
Imports IRanges, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust, genefilter, nlme, reshape
Suggests IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, minfiData(>= 0.4.1), quadprog, FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest
System Requirements
URL
Depends On Me ChAMP, CopyNumber450k, CopyNumber450kData, DMRcate, FlowSorted.Blood.450k, FlowSorted.DLPFC.450k, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, methylumi, minfiData, shinyMethyl
Imports Me MethylAid, methylumi
Suggests Me

Package Downloads

Package Source minfi_1.11.10.tar.gz
Windows Binary minfi_1.11.10.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) minfi_1.11.10.tgz
Mac OS X 10.9 (Mavericks) minfi_1.11.10.tgz
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