minfi

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

Analyze Illumina Infinium DNA methylation arrays

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DOI: 10.18129/B9.bioc.minfi

Bioconductor version: Release (3.22)

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 "4.5") 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 1.56.0

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

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, 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_1.56.0.tar.gz

Windows Binary (x86_64) minfi_1.55.1.zip

macOS Binary (x86_64) minfi_1.56.0.tgz

macOS Binary (arm64) minfi_1.56.0.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/

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