To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("R453Plus1Toolbox")

In most cases, you don't need to download the package archive at all.

R453Plus1Toolbox

This package is for version 3.2 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: 3.2

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("R453Plus1Toolbox")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("R453Plus1Toolbox")
PDF 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 1.20.0
In Bioconductor since BioC 2.7 (R-2.12) (5.5 years)
License LGPL-3
Depends R (>= 2.12.0), methods, VariantAnnotation, Biostrings, Biobase
Imports utils, grDevices, graphics, stats, tools, xtable, R2HTML, TeachingDemos, BiocGenerics, S4Vectors, IRanges, XVector, GenomicRanges, SummarizedExperiment, biomaRt, BSgenome, Rsamtools, ShortRead
LinkingTo
Suggests rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source R453Plus1Toolbox_1.20.0.tar.gz
Windows Binary R453Plus1Toolbox_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) R453Plus1Toolbox_1.20.0.tgz
Mac OS X 10.9 (Mavericks) R453Plus1Toolbox_1.20.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/R453Plus1Toolbox/tree/release-3.2
Package Short Url http://bioconductor.org/packages/R453Plus1Toolbox/
Package Downloads Report Download Stats

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