DESCRIPTION

Package: methylKit
Type: Package
Title: DNA methylation analysis from high-throughput
    bisulfite sequencing results
Version: 1.29.1
Author: Altuna Akalin [aut, cre], Matthias Kormaksson [aut], 
    Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], 
    Alexander Blume [aut], Katarzyna Wreczycka [ctb]
Maintainer: Altuna Akalin <aakalin@gmail.com>, Alexander Blume 
    <alex.gos90@gmail.com>
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: https://github.com/al2na/methylKit
BugReports: https://github.com/al2na/methylKit/issues
LazyLoad: yes
NeedsCompilation: yes
LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc
SystemRequirements: GNU make
biocViews: DNAMethylation, Sequencing, MethylSeq
Depends:
    R (>= 3.5.0),
    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: 7.1.1