To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("minfi")

In most cases, you don't need to download the package archive at all.

minfi

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see minfi.

Analyze Illumina's 450k methylation arrays

Bioconductor version: 3.1

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

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("minfi")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("minfi")
PDF R Script Minfi Guide
PDF Reference Manual
Text NEWS

Details

biocViews DNAMethylation, DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.14.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), lattice, GenomicRanges, Biostrings, utils, bumphunter(>= 1.1.9)
Imports S4Vectors, GenomeInfoDb, IRanges, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust, genefilter, nlme, reshape, MASS, quadprog, GEOquery
LinkingTo
Suggests IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, minfiData(>= 0.4.1), FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest, data.table
SystemRequirements
Enhances
URL https://github.com/kasperdanielhansen/minfi
Depends On Me ChAMP, conumee, CopyNumber450k, CopyNumber450kData, DMRcate, ENmix, FlowSorted.Blood.450k, FlowSorted.DLPFC.450k, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, methylumi, minfiData, shinyMethyl
Imports Me MethylAid, methylumi, missMethyl, quantro, skewr
Suggests Me RnBeads
Build Report

Package Archives

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

Package Source minfi_1.14.0.tar.gz
Windows Binary minfi_1.14.0.zip
Mac OS X 10.6 (Snow Leopard) minfi_1.14.0.tgz
Mac OS X 10.9 (Mavericks) minfi_1.14.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/minfi/tree/release-3.1
Package Short Url http://bioconductor.org/packages/minfi/
Package Downloads Report Download Stats

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