minfi

DOI: 10.18129/B9.bioc.minfi    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see minfi.

Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel
Version	1.28.4
In Bioconductor since	BioC 2.9 (R-2.14) (7.5 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(>= 0.7.38), HDF5Array, BiocParallel
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/hansenlab/minfi
BugReports	https://github.com/hansenlab/minfi/issues
Depends On Me	bigmelon, ChAMP, compartmap, conumee, DMRcate, ENmix, FlowSorted.Blood.450k, FlowSorted.Blood.EPIC, FlowSorted.CordBlood.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, methylationArrayAnalysis, methylumi, methyvimData, minfiData, minfiDataEPIC, REMP, shinyMethyl
Imports Me	funtooNorm, MEAL, MethylAid, methylumi, methyvim, missMethyl, quantro, skewr
Suggests Me	brgedata, CopyNeutralIMA, epivizrChart, Harman, mCSEA, MultiDataSet, RnBeads, sesame
Links To Me
Build Report

Package Archives

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

Source Package	minfi_1.28.4.tar.gz
Windows Binary	minfi_1.28.4.zip
Mac OS X 10.11 (El Capitan)	minfi_1.28.4.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	http://bioconductor.org/packages/minfi/
Package Downloads Report	Download Stats