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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("R453Plus1Toolbox")
In most cases, you don't need to download the package archive at all.
R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System.
Bioconductor version: 3.0
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:
source("http://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")
| R Script | A package for importing and analyzing data from Roche's Genome Sequencer System | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, QualityControl, ReportWriting, Sequencing, Software, Visualization |
| Version | 1.16.0 |
| 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 |
| 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_1.16.0.tar.gz |
| Windows Binary | R453Plus1Toolbox_1.16.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | R453Plus1Toolbox_1.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | R453Plus1Toolbox_1.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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