methylKit
This is the development version of methylKit; for the stable release version, see methylKit.
DNA methylation analysis from high-throughput bisulfite sequencing results
Bioconductor version: Development (3.24)
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 Blume [aut], Katarzyna Wreczycka [ctb]
Maintainer: Altuna Akalin <aakalin at gmail.com>, Alexander Blume <alex.gos90 at gmail.com>
citation("methylKit")):Altuna Akalin, Matthias Kormaksson, Sheng Li, Adrian Bierling, Alexander Blume. methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results. doi:10.18129/B9.bioc.methylKit, R package version 1.39.0, https://bioconductor.org/packages/methylKit.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("methylKit")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("methylKit")| methylKit: User Guide v`r packageVersion('methylKit')` | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, MethylSeq, Sequencing, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils |
| System Requirements | GNU make |
| URL | https://github.com/al2na/methylKit |
| Bug Reports | https://github.com/al2na/methylKit/issues |
See More
| Suggests | testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager |
| Linking To | Rcpp, Rhtslib (>= 1.13.1) |
| Enhances | |
| Depends On Me | |
| Imports Me | deconvR, methInheritSim, methylInheritance |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylKit_1.39.0.tar.gz |
| Windows Binary (x86_64) | methylKit_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | methylKit_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | methylKit_1.39.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylKit |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylKit |
| Package Short Url | https://bioconductor.org/packages/methylKit/ |
| Package Downloads Report | Download Stats |