minfi

This is thedevelopment version of minfi; for the stable release version, seeminfi.

Analyze Illumina Infinium DNA methylation arrays

DOI: 10.18129/B9.bioc.minfi

Bioconductor version: Development (3.23)

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, entercitation("minfi")):

Installation

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

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("minfi")

For older versions of R, please refer to the appropriateBioconductor 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	1.57.0
In Bioconductor since	BioC 2.9 (R-2.14) (14 years)
License	Artistic-2.0
Depends	methods,BiocGenerics(>= 0.15.3),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	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,MEAL,MEAT,MethylAid,methylCC,methylclock,methylumi,missMethyl,quantro,recountmethylation,shinyepico,shinyMethyl,skewr,HiBED,EMAS
Suggests Me	dmGsea,epivizr,epivizrChart,GeoTcgaData,Harman,mCSEA,MultiDataSet,planet,RnBeads,brgedata,epimutacionsData,GSE159526,CimpleG,MLML2R
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	minfi_1.57.0.tar.gz
Windows Binary (x86_64)	minfi_1.57.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	minfi_1.57.0.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

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