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>

Citation (from within R, enter citation("minfi")):

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

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