methylSig
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Bioconductor version: Release (3.20)
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 "4.4") 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 | 1.18.0 |
In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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_1.18.0.tar.gz |
Windows Binary (x86_64) | methylSig_1.18.0.zip (64-bit only) |
macOS Binary (x86_64) | methylSig_1.18.0.tgz |
macOS Binary (arm64) | methylSig_1.17.0.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 |