methylSig
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see methylSig.
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Bioconductor version: 3.16
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")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.10.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, 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_1.10.0.tar.gz |
| Windows Binary | methylSig_1.10.0.zip |
| macOS Binary (x86_64) | methylSig_1.10.0.tgz |
| macOS Binary (arm64) | methylSig_1.10.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |