Package: methylKit
Type: Package
Title: DNA methylation analysis from high-throughput bisulfite
        sequencing results
Version: 1.39.0
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)
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), Seqinfo, 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
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:43:51 UTC
RemoteUrl: https://github.com/bioc/methylKit
RemoteRef: HEAD
RemoteSha: ac7f68d4b40ea0dd51073db8085a68b51544d748
Packaged: 2026-06-23 15:56:21 UTC; root