Package: methylKit
Type: Package
Title: DNA methylation analysis from high-throughput bisulfite
        sequencing results
Version: 1.34.0
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), 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
git_url: https://git.bioconductor.org/packages/methylKit
git_branch: RELEASE_3_21
git_last_commit: 3610aaf
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
Packaged: 2025-04-16 01:53:44 UTC; biocbuild
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:52:17 UTC; windows
Archs: x64
