minfi

DOI: 10.18129/B9.bioc.minfi  

Analyze Illumina Infinium DNA methylation arrays

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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 1.44.0
In Bioconductor since BioC 2.9 (R-2.14) (11.5 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
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 BeadSorted.Saliva.EPIC, bigmelon, ChAMP, conumee, FlowSorted.Blood.450k, FlowSorted.Blood.EPIC, FlowSorted.CordBlood.450k, FlowSorted.CordBloodCombined.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, minfiData, minfiDataEPIC, REMP, shinyMethyl
Imports Me deconvR, DMRcate, ENmix, epimutacions, funtooNorm, MEAL, MEAT, MethylAid, methylCC, methylclock, methylumi, missMethyl, quantro, recountmethylation, shinyepico, skewr
Suggests Me brgedata, CopyNeutralIMA, EnMCB, epimutacionsData, epivizr, epivizrChart, GSE159526, Harman, mCSEA, MultiDataSet, planet, RnBeads
Links To Me
Build Report  

Package Archives

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

Source Package minfi_1.44.0.tar.gz
Windows Binary minfi_1.44.0.zip (64-bit only)
macOS Binary (x86_64) minfi_1.44.0.tgz
macOS Binary (arm64) minfi_1.44.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: