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 (3.21)
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("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 | R Script | |
| Reference Manual |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Software, Visualization |
| Version | 1.57.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (14 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
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | R453Plus1Toolbox_1.57.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |