msgbsR

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see msgbsR.

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

Bioconductor version: 3.19

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")):

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.

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

biocViews	DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, Software
Version	1.28.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 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

Suggests	roxygen2, BSgenome.Rnorvegicus.UCSC.rn6
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

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

Source Package	msgbsR_1.28.0.tar.gz
Windows Binary (x86_64)	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