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msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions

Bioconductor version: Release (3.19)

Pipeline for the anaysis of a MS-GBS experiment.

Author: Benjamin Mayne

Maintainer: Benjamin Mayne <benjamin.mayne at>

Citation (from within R, enter citation("msgbsR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

msgbsR_Example PDF R Script
Reference Manual PDF


biocViews DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, Software
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-2
Depends R (>= 3.5.0), GenomicRanges, methods
Imports BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils
System Requirements
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Suggests roxygen2, BSgenome.Rnorvegicus.UCSC.rn6
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Follow Installation instructions to use this package in your R session.

Source Package msgbsR_1.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) msgbsR_1.28.0.tgz
macOS Binary (arm64) msgbsR_1.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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