methylSig
This is the development version of methylSig; for the stable release version, see methylSig.
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Bioconductor version: Development (3.24)
MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.
Author: Yongseok Park [aut], Raymond G. Cavalcante [aut, cre]
Maintainer: Raymond G. Cavalcante <rcavalca at umich.edu>
citation("methylSig")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("methylSig")
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("methylSig")| Updating methylSig code | HTML | R Script |
| Using methylSig | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, Seqinfo, GenomicRanges, methods, parallel, stats, S4Vectors |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/sartorlab/methylSig/issues |
See More
| Suggests | BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylSig_1.25.0.tar.gz |
| Windows Binary (x86_64) | methylSig_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | methylSig_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | methylSig_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylSig |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylSig |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylSig/ |
| Package Short Url | https://bioconductor.org/packages/methylSig/ |
| Package Downloads Report | Download Stats |