Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: Release (2.9)

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")

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

    citation("Biostrings")

Documentation

PDF	R Script	A short presentation of the basic classes defined in Biostrings 2
PDF	R Script	Handling probe sequence information
PDF	R Script	Multiple Alignments
PDF	R Script	Pairwise Sequence Alignments
PDF		Reference Manual
Text		NEWS

Details

biocViews	SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation
Depends	R, methods, IRanges
Imports	graphics, methods, stats, utils, IRanges
Suggests	BSgenome, BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures, hgu95av2cdf, affy, affydata, RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me	BSgenome, ChIPpeakAnno, ChIPsim, DECIPHER, GeneRegionScan, R453Plus1Toolbox, REDseq, Rsamtools, ShortRead, VariantAnnotation, altcdfenvs, methVisual, rGADEM, seqbias
Imports Me	AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass, ChIPpeakAnno, ChIPseqR, ChIPsim, DECIPHER, GeneRegionScan, GenomicFeatures, MEDIPS, MEDME, OTUbase, R453Plus1Toolbox, REDseq, Rolexa, Rsamtools, ShortRead, biovizBase, charm, gcrma, genoset, girafe, methVisual, microRNA, oligoClasses, oligo, pdInfoBuilder, rGADEM, rtracklayer
Suggests Me	CSAR, GenomicFeatures, SLGI, annotate, exomeCopy, microRNA, oneChannelGUI, procoil
Version	2.22.0
Since	Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source	Biostrings_2.22.0.tar.gz
Windows Binary	Biostrings_2.22.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Biostrings_2.22.0.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center