Package: methylKit
Type: Package
Title: DNA methylation analysis from high-throughput bisulfite
        sequencing results
Version: 1.0.0
Authors@R: c(person("Altuna", "Akalin", role = c("aut", "cre"),
  	     email = "aakalin@gmail.com"),
	      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"))
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. Perl is needed to read SAM files
    only.
License: Artistic-2.0
URL: http://code.google.com/p/methylkit/
LazyLoad: yes
LinkingTo: Rcpp, Rhtslib, zlibbioc
biocViews: DNAMethylation, Sequencing, MethylSeq
Depends: R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods
Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors,
        GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools, gtools,
        fastseg, rtracklayer, mclust, Rcpp, R.utils, limma, grDevices,
        graphics, stats, utils
Suggests: testthat,knitr, rmarkdown, genomation
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'
        'adjust.methylC.R' 'updateMethObject.R' 'batchControl.R'
        'dataSim.R' 'methylDBClasses.R' 'methylDBFunctions.R'
        'tabix.functions.R' 'methSeg.R' 'diffMethDSS.R'
        'deprecated_defunct.R'
RoxygenNote: 5.0.1
NeedsCompilation: yes
Author: Altuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li
        [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander
        Gosdschan [aut]
Maintainer: Altuna Akalin <aakalin@gmail.com>
Built: R 3.3.2; x86_64-apple-darwin14.5.0; 2017-06-06 14:25:01 UTC; unix
