Analyze Illumina's 450k methylation arrays
Tools for analyzing and visualizing Illumina's 450k array data.
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("Shan", "Andrews", role = "ctb"))
methods, BiocGenerics (>= 0.15.3), Biobase (>= 2.17.8),
lattice, GenomicRanges, SummarizedExperiment (>= 0.3.1),
Biostrings, utils, bumphunter (>= 1.1.9)
IlluminaHumanMethylation450kmanifest (>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
minfiData (>= 0.4.1), FlowSorted.Blood.450k (>= 1.0.1), RUnit,
digest, data.table
S4Vectors, GenomeInfoDb, IRanges, beanplot, RColorBrewer,
nor1mix, siggenes, limma, preprocessCore, illuminaio,
matrixStats, mclust, genefilter, nlme, reshape, MASS, quadprog,
GEOquery, mixOmics
generics.R mset.R rset.R rgset.R gmset.R grset.R utils.R
manifest.R anno.R minfiQC.R getSex.R dmr.R blocks.R plot.R
plotBetasByType.R preprocess.R preprocessSwan.R
preprocessQuantile.R preprocessNoob.R preprocessFunnorm.R qc.R
read.450k.R read.manifest.R bumphunter.R estimateCellCounts.R
gaphunter.R compartments.R
DNAMethylation, Microarray, TwoChannel, DataImport,
Preprocessing, QualityControl
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 Andrews [ctb]