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/
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