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

DOI: 10.18129/B9.bioc.minfi

Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: Release (3.5)

Tools to analyze & visualize Illumina Infinium methylation arrays.

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 V. 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 User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel
Version	1.22.1
In Bioconductor since	BioC 2.9 (R-2.14) (6 years)
License	Artistic-2.0
Depends	methods, BiocGenerics(>= 0.15.3), GenomicRanges, SummarizedExperiment(>= 1.1.6), Biostrings, bumphunter(>= 1.1.9)
Imports	S4Vectors, GenomeInfoDb, Biobase(>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats (>= 0.50.0), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils
LinkingTo
Suggests	IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), minfiData(>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/kasperdanielhansen/minfi
BugReports	https://github.com/kasperdanielhansen/minfi/issues
Depends On Me	bigmelon, ChAMP, conumee, CopyNumber450kData, DMRcate, ENmix, FlowSorted.Blood.450k, FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, FlowSorted.DLPFC.450k, IlluminaHumanMethylation27kanno.ilmn12.hg19, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICanno.ilm10b3.hg19, IlluminaHumanMethylationEPICmanifest, methylumi, minfiData, minfiDataEPIC, REMP, shinyMethyl
Imports Me	ELMER, funtooNorm, MEAL, MethylAid, methylumi, missMethyl, quantro, skewr
Suggests Me	Harman, MultiDataSet, RnBeads
Build Report

Package Archives

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

Source Package	minfi_1.22.1.tar.gz
Windows Binary	minfi_1.22.1.zip
Mac OS X 10.11 (El Capitan)	minfi_1.22.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/minfi
Package Short Url	http://bioconductor.org/packages/minfi/
Package Downloads Report	Download Stats

Documentation »

Bioconductor

Package vignettes and manuals.
Workflows for learning and use.
Course and conference material.
Videos.
Community resources and tutorials.

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Support site - for questions about Bioconductor packages
Bioc-devel mailing list - for package developers