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minfi

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

Analyze Illumina Infinium DNA methylation arrays


Bioconductor version: Development (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")):

Installation

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


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

# The following initializes usage of Bioc devel
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

Details

biocViews DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel
Version 1.51.0
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
URL https://github.com/hansenlab/minfi
Bug Reports https://github.com/hansenlab/minfi/issues
See More
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, 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_1.51.0.tar.gz
Windows Binary minfi_1.51.0.zip (64-bit only)
macOS Binary (x86_64) minfi_1.51.0.tgz
macOS Binary (arm64) minfi_1.51.0.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