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R453Plus1Toolbox

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


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("R453Plus1Toolbox")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
A package for importing and analyzing data from Roche's Genome Sequencer System PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version 1.52.0
In Bioconductor since BioC 2.7 (R-2.12) (13.5 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)
System Requirements
URL
See More
Suggests rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2
Linking To
Enhances
Depends On Me
Imports Me
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Package Archives

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

Source Package R453Plus1Toolbox_1.52.0.tar.gz
Windows Binary R453Plus1Toolbox_1.52.0.zip
macOS Binary (x86_64) R453Plus1Toolbox_1.52.0.tgz
macOS Binary (arm64) R453Plus1Toolbox_1.52.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/R453Plus1Toolbox
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/R453Plus1Toolbox
Bioc Package Browser https://code.bioconductor.org/browse/R453Plus1Toolbox/
Package Short Url https://bioconductor.org/packages/R453Plus1Toolbox/
Package Downloads Report Download Stats