R453Plus1Toolbox

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("R453Plus1Toolbox")

To cite this package in a publication, start R and enter:

    citation("R453Plus1Toolbox")

Documentation

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 1.14.0
In Bioconductor since BioC 2.7 (R-2.12)
License LGPL-3
Depends R (>= 2.12.0), Biobase, Biostrings, GenomicRanges
Imports BiocGenerics(>= 0.1.3), biomaRt, BSgenome, IRanges, XVector, methods, R2HTML, Rsamtools, ShortRead, VariantAnnotation, xtable, tools, TeachingDemos
Suggests rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source R453Plus1Toolbox_1.14.0.tar.gz
Windows Binary R453Plus1Toolbox_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) R453Plus1Toolbox_1.14.0.tgz
Mac OS X 10.9 (Mavericks)
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