minfi

This is the released version of minfi; for the devel version, see minfi.

Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: Release (3.20)

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 gmail.com>

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

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA (2014). “Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.” Bioinformatics, 30(10), 1363–1369. doi:10.1093/bioinformatics/btu049.

Maksimovic J, Gordon L, Oshlack A (2012). “SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips.” Genome Biology, 13(6), R44. doi:10.1186/gb-2012-13-6-r44.

Fortin J, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD (2014). “Functional normalization of 450k methylation array data improves replication in large cancer studies.” Genome Biology, 15(12), 503. doi:10.1186/s13059-014-0503-2.

Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD (2013). “Low-level processing of Illumina Infinium DNA Methylation BeadArrays.” Nucleic Acids Research, 41(7), e90. doi:10.1093/nar/gkt090.

Fortin J, Hansen KD (2015). “Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.” Genome Biology, 16, 180. doi:10.1186/s13059-015-0741-y.

Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD (2016). “'Gap hunting' to characterize clustered probe signals in Illumina methylation array data.” Epigenetics & Chromatin, 9, 56. doi:10.1186/s13072-016-0107-z.

Fortin J, Triche TJ, Hansen KD (2017). “Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.” Bioinformatics, 33(4). doi:10.1093/bioinformatics/btw691.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("minfi")

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

Documentation

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

browseVignettes("minfi")

minfi User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel
Version	1.52.1
In Bioconductor since	BioC 2.9 (R-2.14) (13.5 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
URL	https://github.com/hansenlab/minfi
Bug Reports	https://github.com/hansenlab/minfi/issues

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
Enhances
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, IlluminaHumanMethylationMSAanno.ilm10a1.hg38, IlluminaHumanMethylationMSAmanifest, 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
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	minfi_1.52.1.tar.gz
Windows Binary (x86_64)	minfi_1.52.1.zip
macOS Binary (x86_64)	minfi_1.52.1.tgz
macOS Binary (arm64)	minfi_1.52.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/minfi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/minfi
Bioc Package Browser	https://code.bioconductor.org/browse/minfi/
Package Short Url	https://bioconductor.org/packages/minfi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.20	Source Archive