methylSig

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see methylSig.

MethylSig: Differential Methylation Testing for WGBS and RRBS Data

Bioconductor version: 3.21

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 (from within R, enter citation("methylSig")):

Installation

To install this package, start R (version "4.5") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, DifferentialMethylation, Epigenetics, MethylSeq, Regression, Software

Version 1.20.0

In Bioconductor since BioC 3.11 (R-4.0) (5.5 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

Suggests BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr

Linking To

Enhances

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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methylSig_1.20.0.tar.gz

Windows Binary (x86_64) methylSig_1.20.0.zip (64-bit only)

macOS Binary (x86_64) methylSig_1.20.0.tgz

macOS Binary (arm64) methylSig_1.20.0.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/

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