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DESCRIPTION
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Package: methylKit
Type: Package
Title: DNA methylation analysis from high-throughput
bisulfite sequencing results
Version: 1.13.1
Authors@R: c(person("Altuna", "Akalin", role = c("aut", "cre"),
email = "[email protected]"),
person("Matthias","Kormaksson", role = "aut"),
person("Sheng","Li", role = "aut"),
person("Arsene", "Wabo", role = "ctb"),
person("Adrian", "Bierling", role= "aut"),
person("Alexander","Gosdschan", role="aut"),
person("Katarzyna","Wreczycka", role="ctb"))
Author: Altuna Akalin [aut, cre], Matthias Kormaksson [aut],
Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut],
Alexander Gosdschan [aut]
Maintainer: Altuna Akalin <[email protected]>, Alexander Gosdschan
Description: methylKit is an R package for DNA methylation analysis and
annotation from high-throughput bisulfite sequencing. The package is
designed to deal with sequencing data from RRBS and its variants, but also
target-capture methods and whole genome bisulfite sequencing. It also has
functions to analyze base-pair resolution 5hmC data from experimental
protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be
performed directly from Bismark aligned BAM files.
License: Artistic-2.0
URL: http://code.google.com/p/methylkit/
LazyLoad: yes
NeedsCompilation: yes
LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc
SystemRequirements: GNU make
biocViews: DNAMethylation, Sequencing, MethylSeq
Depends:
R (>= 3.3.0),
GenomicRanges (>= 1.18.1),
methods
Imports:
IRanges,
data.table (>= 1.9.6),
parallel,
S4Vectors (>= 0.13.13),
GenomeInfoDb,
KernSmooth,
qvalue,
emdbook,
Rsamtools,
gtools,
fastseg,
rtracklayer,
mclust,
mgcv,
Rcpp,
R.utils,
limma,
grDevices,
graphics,
stats,
utils
Suggests:
testthat (>= 2.1.0),
knitr,
rmarkdown,
genomation,
BiocManager
VignetteBuilder: knitr
Collate:
'methylKit.R'
'backbone.R'
'diffMeth.R'
'clusterSamples.R'
'regionalize.R'
'processBismarkAln.R'
'RcppExports.R'
'document_data.R'
'bedgraph.R'
'reorganize.R'
'percMethylation.R'
'normalizeCoverage.R'
'pool.R'
'adjustMethylC.R'
'updateMethObject.R'
'batchControl.R'
'dataSim.R'
'methylDBClasses.R'
'methylDBFunctions.R'
'tabix.functions.R'
'methSeg.R'
'diffMethDSS.R'
'deprecated_defunct.R'
'onUnload.R'
RoxygenNote: 6.1.1