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msgbsR

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 adelaide.edu.au>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("msgbsR")

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("msgbsR")
msgbsR_Example PDF R Script
Reference Manual PDF

Details

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
URL
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Suggests roxygen2, BSgenome.Rnorvegicus.UCSC.rn6
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Package Archives

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

Source Package msgbsR_1.28.0.tar.gz
Windows Binary msgbsR_1.28.0.zip (64-bit only)
macOS Binary (x86_64) msgbsR_1.28.0.tgz
macOS Binary (arm64) msgbsR_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/msgbsR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/msgbsR
Bioc Package Browser https://code.bioconductor.org/browse/msgbsR/
Package Short Url https://bioconductor.org/packages/msgbsR/
Package Downloads Report Download Stats