DOI: 10.18129/B9.bioc.methylKit  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see methylKit.

DNA methylation analysis from high-throughput bisulfite sequencing results

Bioconductor version: 3.17

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.

Author: Altuna Akalin [aut, cre], Matthias Kormaksson [aut], Sheng Li [aut], Arsene Wabo [ctb], Adrian Bierling [aut], Alexander Gosdschan [aut]

Maintainer: Altuna Akalin <aakalin at>, Alexander Gosdschan <alex.gos90 at>

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biocViews DNAMethylation, MethylSeq, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License Artistic-2.0
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
LinkingTo Rcpp, Rhtslib(>= 1.13.1), zlibbioc
Suggests testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager
SystemRequirements GNU make
Depends On Me
Imports Me deconvR, MethCP, methInheritSim, methylInheritance
Suggests Me
Links To Me
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