Package: methylumi
Type: Package
Title: Handle Illumina methylation data
Version: 2.55.0
Date: 2021-10-27
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
        matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
        SummarizedExperiment, Biobase, graphics, lattice, annotate,
        genefilter, AnnotationDbi, minfi, stats4, illuminaio,
        GenomicFeatures
Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
        parallel, rtracklayer, Biostrings, TCGAMethylation450k,
        IlluminaHumanMethylation450kanno.ilmn12.hg19,
        FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
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 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: knitr
BugReports: https://github.com/seandavi/methylumi/issues/new
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.1.2
git_url: https://git.bioconductor.org/packages/methylumi
git_branch: devel
git_last_commit: 7d7333d
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 00:20:54 UTC; biocbuild
Built: R 4.5.0; ; 2025-06-05 13:23:37 UTC; windows
