Package: minfi
Version: 1.57.0
Title: Analyze Illumina Infinium DNA methylation arrays
Description: Tools to analyze & visualize Illumina Infinium methylation arrays.
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),
                    email = "kasperdanielhansen@gmail.com"),
             person("Martin", "Aryee", role = "aut"),
             person(c("Rafael", "A."), "Irizarry", role = "aut"),
             person(c("Andrew", "E."), "Jaffe", role = "ctb"),
             person("Jovana", "Maksimovic", role = "ctb"),
             person(c("E.", "Andres"), "Houseman", role = "ctb"),
             person("Jean-Philippe", "Fortin", role = "ctb"),
             person("Tim", "Triche", role = "ctb"),
             person(c("Shan", "V."), "Andrews", role = "ctb"),
             person(c("Peter", "F."), "Hickey", role = "ctb"))
Depends:  methods,
	  BiocGenerics (>= 0.15.3),
	  GenomicRanges (>= 1.61.1),
	  SummarizedExperiment (>= 1.39.1),
	  Biostrings (>= 2.77.2),
	  bumphunter (>= 1.1.9)
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
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
Collate:  AllGenerics.R
	  MethylSet-class.R
	  RatioSet-class.R
	  RGChannelSet-class.R
	  RGChannelSetExtended-class.R
	  GenomicMethylSet-class.R
	  GenomicRatioSet-class.R
	  eSet_methods.R
	  utils.R
	  IlluminaMethylationManifest-class.R
	  IlluminaMethylationAnnotation-class.R
	  minfiQC.R
	  getSex.R
	  dmpFinder.R
	  blocks.R
	  plot.R
	  plotBetasByType.R
	  preprocessRaw.R
	  preprocessIllumina.R
	  detectionP.R
	  preprocessSwan.R
	  preprocessQuantile.R
	  preprocessNoob.R
	  preprocessFunnorm.R
	  qc.R
	  read.450k.R
	  read.meth.R
	  read.meth2.R
	  read.geo.R
	  read.manifest.R
	  bumphunter.R
	  estimateCellCounts.R
	  gaphunter.R
	  compartments.R
	  combineArrays.R
	  DelayedArray_utils.R
VignetteBuilder: knitr
License: Artistic-2.0
URL: https://github.com/hansenlab/minfi
BugReports: https://github.com/hansenlab/minfi/issues
LazyData: yes
biocViews: ImmunoOncology, DNAMethylation, DifferentialMethylation, Epigenetics, Microarray, MethylationArray,
	   MultiChannel, TwoChannel, DataImport, Normalization, Preprocessing, QualityControl
git_url: https://git.bioconductor.org/packages/minfi
git_branch: devel
git_last_commit: 36249fb
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
