R453Plus1Toolbox

This is the released version of R453Plus1Toolbox; for the devel version, see R453Plus1Toolbox.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7

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

Bioconductor version: Release (3.23)

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")):

Hans-Ulrich Klein, Christoph Bartenhagen, Christian Ruckert. R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System. doi:10.18129/B9.bioc.R453Plus1Toolbox, R package version 1.62.0, https://bioconductor.org/packages/R453Plus1Toolbox.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Software, Visualization
Version	1.62.0
In Bioconductor since	BioC 2.7 (R-2.12) (16 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

Suggests	rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	R453Plus1Toolbox_1.62.0.tar.gz
Windows Binary (x86_64)	R453Plus1Toolbox_1.62.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	R453Plus1Toolbox_1.62.0.tgz
macOS Binary (sonoma-arm64)	R453Plus1Toolbox_1.62.0.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	https://bioconductor.org/packages/R453Plus1Toolbox/
Package Downloads Report	Download Stats