Package: methylumi
Type: Package
Title: Handle Illumina methylation data
Version: 2.59.3
Date: 2026-08-14
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Depends: Biobase, methods, R (>= 4.0), scales, reshape2, ggplot2,
        matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
        SummarizedExperiment, Biobase, graphics, grDevices, stats,
        utils, lattice, annotate, genefilter, AnnotationDbi, minfi,
        stats4, illuminaio, GenomicFeatures, BiocParallel
Suggests: lumi, limma, SQN, MASS, rtracklayer, Biostrings, quarto,
        TCGAMethylation450k,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens,
        TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, testthat (>= 3.0.0)
biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl,
        CpGIsland
Maintainer: Sean Davis <seandavi@gmail.com>
Description: This package provides classes for holding and manipulating
        Illumina methylation data.  Based on eSet, it can contain MIAME
        information, sample information, feature information, and
        multiple matrices of data.  An "intelligent" import function,
        methylumiR can read the Illumina text files and create a
        MethyLumiSet. methylumIDAT can directly read raw IDAT files
        from HumanMethylation27 and HumanMethylation450 microarrays.
        Normalization, background correction, and quality control
        features for GoldenGate, Infinium, and Infinium HD arrays are
        also included.
Collate: AllGenerics.R MethyLumiSet-class.R MethyLumiM-class.R
        MoreGenerics.R Methods.R bgcorr.R coercions.R data.R
        detectionpval.R featureFilter.R mclapply_replace.R
        methylData-class.R methylumIDAT.R methylumiCSV.R methylumiR.R
        normalization.R plotNegOob.R qc.probe.plot.R readIDAT2.R
        stripMethyLumiSet.R utilities.R varFilter.R
VignetteBuilder: quarto
URL: https://seandavi.github.io/methylumi/,
        https://github.com/seandavi/methylumi
BugReports: https://github.com/seandavi/methylumi/issues
License: GPL-2
Encoding: UTF-8
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-14 16:33:14 UTC
RemoteUrl: https://github.com/bioc/methylumi
RemoteRef: HEAD
RemoteSha: 4232eaf043694b8b8e2bfe1095f03185be39a8af
NeedsCompilation: no
Packaged: 2026-10-13 13:31:33 UTC; root