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

Analyze Illumina's 450k methylation arrays

Bioconductor version: Development (3.3)

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 Minfi Guide
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel
Version 1.17.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.15.3), Biobase(>= 2.17.8), lattice, GenomicRanges, SummarizedExperiment(>= 0.3.1), 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, mixOmics
LinkingTo
Suggests IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), minfiData(>= 0.4.1), FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest, data.table
SystemRequirements
Enhances
URL https://github.com/kasperdanielhansen/minfi
BugReports https://github.com/kasperdanielhansen/minfi/issues
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 ELMER, MEAL, 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_1.17.0.tar.gz
Windows Binary minfi_1.17.0.zip
Mac OS X 10.6 (Snow Leopard) minfi_1.15.11.tgz
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/minfi
Package Short Url http://bioconductor.org/packages/minfi/
Package Downloads Report Download Stats

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