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DESCRIPTION
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DESCRIPTION
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Package: minfi
Version: 1.49.3
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 = "[email protected]"),
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,
SummarizedExperiment (>= 1.1.6),
Biostrings,
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,
GenomeInfoDb,
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