minfi
Analyze Illumina Infinium DNA methylation arrays
Bioconductor version: 3.23 · Package version: 1.58.0
Tools to analyze & visualize Illumina Infinium methylation arrays.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("minfi")Details
| Maintainer | Kasper Daniel Hansen <kasperdanielhansen@gmail.com> |
| 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] |
| License | Artistic-2.0 |
| URL | https://github.com/hansenlab/minfi |
| Bug Reports | https://github.com/hansenlab/minfi/issues |
| Downloads rank | 3038 |
| Source branch | RELEASE_3_23 |
| biocViews | DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Software, TwoChannel |
Documentation
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Dependencies
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
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
Reverse dependencies
Depends On Me (27): 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, IlluminaHumanMethylationEPICv2anno.20a1.hg38, IlluminaHumanMethylationEPICv2manifest, IlluminaHumanMethylationMSAanno.ilm10a1.hg38, IlluminaHumanMethylationMSAmanifest, methylationArrayAnalysis, methylumi, minfiData, minfiDataEPIC, REMP
Imports Me (19): deconvR, DMRcate, ENmix, epimutacions, funtooNorm, HiBED, iNETgrate, MEAL, MEAT, MethylAid, methylCC, methylclock, methylumi, missMethyl, quantro, recountmethylation, shinyepico, shinyMethyl, skewr
Suggests Me (15): brgedata, CimpleG, CopyNeutralIMA, dmGsea, epimutacionsData, epivizr, epivizrChart, GeoTcgaData, GSE159526, Harman, mCSEA, MLML2R, MultiDataSet, planet, RnBeads