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Bioconductor - R453Plus1Toolbox (development version)

R453Plus1Toolbox

This is the development version of R453Plus1Toolbox; for the stable release version, see R453Plus1Toolbox.

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

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.59.0 In Bioconductor since BioC 2.7 (R-2.12) (14.5 years) License LGPL-3 Depends R (>= 2.12.0), methods, VariantAnnotation(>= 1.25.11), Biostrings(>= 2.47.6), pwalign, 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 Package Archives

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

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