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")):


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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
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
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
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Source Package minfi_1.28.4.tar.gz
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