minfi

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: Development (3.24)

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")):

Kasper Daniel Hansen, Martin Aryee, Rafael A. Irizarry. minfi: Analyze Illumina Infinium DNA methylation arrays. doi:10.18129/B9.bioc.minfi, R package version 1.59.1, https://bioconductor.org/packages/minfi.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.59.1
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	Artistic-2.0
Depends	methods, BiocGenerics (>= 0.59.3), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), bumphunter (>= 1.1.9)
Imports	S4Vectors, Seqinfo, 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	BeadSorted.Saliva.EPIC, bigmelon, ChAMP, conumee, FlowSorted.Blood.450k, FlowSorted.CordBlood.450k, FlowSorted.CordBloodCombined.450k, FlowSorted.CordBloodNorway.450k, FlowSorted.DLPFC.450k, 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, methylationArrayAnalysis, methylumi, minfiData, minfiDataEPIC, REMP
Imports Me	deconvR, DMRcate, dnaEPICO, ENmix, epimutacions, FlowSorted.Blood.EPIC, funtooNorm, HiBED, iNETgrate, MEAL, MEAT, MethylAid, methylCC, methylumi, missMethyl, quantro, recountmethylation, shinyepico, shinyMethyl, skewr
Suggests Me	brgedata, CimpleG, CopyNeutralIMA, dmGsea, epimutacionsData, epivizr, epivizrChart, GeoTcgaData, GSE159526, Harman, mCSEA, methylclock, MLML2R, MultiDataSet, planet, RnBeads
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	minfi_1.59.1.tar.gz
Windows Binary (x86_64)	minfi_1.59.1.zip
macOS Binary (big-sur-x86_64)	minfi_1.59.1.tgz
macOS Binary (sonoma-arm64)	minfi_1.59.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/minfi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/minfi
Package Short Url	https://bioconductor.org/packages/minfi/
Package Downloads Report	Download Stats