R453Plus1Toolbox

DOI: 10.18129/B9.bioc.R453Plus1Toolbox    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see R453Plus1Toolbox.

A package for importing and analyzing data from Roche's Genome Sequencer System

Bioconductor version: 3.8

The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.

Author: Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert

Maintainer: Hans-Ulrich Klein <h.klein at uni-muenster.de>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("R453Plus1Toolbox")

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("R453Plus1Toolbox")

 

PDF	R Script	A package for importing and analyzing data from Roche's Genome Sequencer System
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version	1.32.0
In Bioconductor since	BioC 2.7 (R-2.12) (8.5 years)
License	LGPL-3
Depends	R (>= 2.12.0), methods, VariantAnnotation(>= 1.25.11), Biostrings(>= 2.47.6), Biobase
Imports	utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), XVector, GenomicRanges(>= 1.31.8), SummarizedExperiment, biomaRt, BSgenome(>= 1.47.3), Rsamtools, ShortRead(>= 1.37.1)
LinkingTo
Suggests	rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2
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	R453Plus1Toolbox_1.32.0.tar.gz
Windows Binary	R453Plus1Toolbox_1.32.0.zip
Mac OS X 10.11 (El Capitan)	R453Plus1Toolbox_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/R453Plus1Toolbox
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/R453Plus1Toolbox
Package Short Url	http://bioconductor.org/packages/R453Plus1Toolbox/
Package Downloads Report	Download Stats