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Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: Release (3.19)

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], Peter F. Hickey [ctb]

Maintainer: Kasper Daniel Hansen <kasperdanielhansen at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

minfi User's Guide HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel
Version 1.50.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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(>= 0.23.2), DelayedMatrixStats(>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray(>= 0.15.16), HDF5Array, BiocParallel
System Requirements
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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, tools
Linking To
Depends On Me bigmelon, ChAMP, conumee, methylumi, REMP, IlluminaHumanMethylation27kanno.ilmn12.hg19, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICanno.ilm10b3.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2anno.20a1.hg38, IlluminaHumanMethylationEPICv2manifest, BeadSorted.Saliva.EPIC, FlowSorted.Blood.450k, FlowSorted.Blood.EPIC, FlowSorted.CordBlood.450k, FlowSorted.CordBloodCombined.450k, FlowSorted.CordBloodNorway.450k, FlowSorted.DLPFC.450k, minfiData, minfiDataEPIC, methylationArrayAnalysis
Imports Me deconvR, DMRcate, epimutacions, funtooNorm, iNETgrate, MEAL, MEAT, MethylAid, methylCC, methylclock, methylumi, missMethyl, quantro, recountmethylation, shinyepico, shinyMethyl, skewr, HiBED, EMAS
Suggests Me epivizr, epivizrChart, GeoTcgaData, Harman, mCSEA, MultiDataSet, planet, RnBeads, brgedata, epimutacionsData, GSE159526, MLML2R
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