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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: