msgbsR

DOI: 10.18129/B9.bioc.msgbsR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see msgbsR.

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

Bioconductor version: 3.9

Pipeline for the anaysis of a MS-GBS experiment.

Author: Benjamin Mayne

Maintainer: Benjamin Mayne <benjamin.mayne at adelaide.edu.au>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	msgbsR_Example
PDF		Reference Manual

Details

biocViews	DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, Software
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL-2
Depends	R (>= 3.4), GenomicRanges, methods
Imports	BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils
LinkingTo
Suggests	roxygen2, BSgenome.Rnorvegicus.UCSC.rn6
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	msgbsR_1.8.0.tar.gz
Windows Binary	msgbsR_1.8.0.zip
Mac OS X 10.11 (El Capitan)	msgbsR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msgbsR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msgbsR
Package Short Url	https://bioconductor.org/packages/msgbsR/
Package Downloads Report	Download Stats