Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: Release (2.7)

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy

Maintainer: H. Pages

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("Biostrings")    

Documentation

PDF	R Script	A short presentation of the basic classes defined in Biostrings 2
PDF	R Script	Efficient genome searching with Biostrings and the BSgenome data packages
PDF	R Script	Handling probe sequence information
PDF	R Script	Multiple Alignments
PDF	R Script	Pairwise Sequence Alignments
PDF	R Script	Some old notes about the vectorization feature of the DNAString() constructor. Not for the end user.

Reference Manual

Details

biocViews	SequenceMatching, Genetics, Infrastructure
Depends	R, methods, IRanges
Imports	graphics, methods, stats, utils, IRanges, Biobase
Suggests	BSgenome, BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3, drosophila2probe, hgu95av2probe, GenomicFeatures, hgu95av2cdf, affy, affydata, RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me	BSgenome, ChIPpeakAnno, ChIPsim, GeneRegionScan, R453Plus1Toolbox, Rsamtools, ShortRead, altcdfenvs, methVisual, rGADEM
Imports Me	AffyCompatible, BCRANK, BioSeqClass, ChIPpeakAnno, ChIPseqR, ChIPsim, GeneRegionScan, GenomicFeatures, MEDIPS, MEDME, OTUbase, R453Plus1Toolbox, Rolexa, Rsamtools, ShortRead, biocDatasets, charm, gcrma, girafe, methVisual, microRNA, oligoClasses, pdInfoBuilder, rGADEM, rtracklayer
Suggests Me	CSAR, GenomicFeatures, SLGI, annotate, microRNA, oneChannelGUI
Version	2.18.4

Package Downloads

Package Source	Biostrings_2.18.4.tar.gz
Windows Binary	Biostrings_2.18.4.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Biostrings_2.18.4.tgz
Package Downloads Report	Download Stats