msgbsR

This is the development version of msgbsR; for the stable release version, see msgbsR.

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

Bioconductor version: Development (3.24)

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")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, Software
Version	1.37.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	GPL-2
Depends	R (>= 3.5.0), GenomicRanges, methods
Imports	BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, Seqinfo, 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

Package Archives

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

Source Package	msgbsR_1.37.0.tar.gz
Windows Binary (x86_64)	msgbsR_1.37.0.zip
macOS Binary (big-sur-x86_64)	msgbsR_1.37.0.tgz
macOS Binary (sonoma-arm64)	msgbsR_1.37.0.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