methylKit
This is the released version of methylKit; for the devel version, see methylKit.
DNA methylation analysis from high-throughput bisulfite sequencing results
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.38.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylKit_1.38.0.tar.gz |
| Windows Binary (x86_64) | methylKit_1.38.0.zip |
| macOS Binary (big-sur-x86_64) | methylKit_1.38.0.tgz |
| macOS Binary (sonoma-arm64) | methylKit_1.38.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylKit |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylKit |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylKit/ |
| Package Short Url | https://bioconductor.org/packages/methylKit/ |
| Package Downloads Report | Download Stats |