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

Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.13

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 <hpages at fhcrc.org>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Biostrings")

 

PDF	R Script	A short presentation of the basic classes defined in Biostrings 2
PDF	R Script	Biostrings Quick Overview
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	DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version	2.30.1
In Bioconductor since	BioC 1.6 (R-2.1) or earlier
License	Artistic-2.0
Depends	R (>= 2.8.0), methods, BiocGenerics(>= 0.5.4), IRanges(>= 1.19.34), XVector(>= 0.1.3)
Imports	graphics, methods, stats, utils, BiocGenerics, IRanges, XVector
Suggests	BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures(>= 1.3.14), hgu95av2cdf, affy, affydata(>= 1.11.5), RUnit
System Requirements
URL
Depends On Me	altcdfenvs, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, cleaver, CorMut, DASiR, DECIPHER, deepSNV, easyRNASeq, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, GeneRegionScan, genomes, harbChIP, iPAC, JASPAR2014, methVisual, minfi, MotifDb, motifRG, oligo, oneChannelGUI, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Roleswitch, Rsamtools, rSFFreader, RSVSim, SCAN.UPC, seqbias, ShortRead, spliceSites, triplex, waveTiling
Imports Me	AffyCompatible, AllelicImbalance, ArrayExpressHTS, BCRANK, BioSeqClass, biovizBase, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, cobindR, customProDB, dagLogo, DECIPHER, ensemblVEP, gcrma, GeneRegionScan, GenomicFeatures, girafe, gmapR, Gviz, gwascat, h5vc, HiTC, HTSeqGenie, KEGGREST, MEDIPS, MEDME, methVisual, microRNA, motifRG, MotIV, oligoClasses, OTUbase, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.atdschip.tiling, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.1.st, pd.rn.u34, pd.s.aureus, pd.soybean, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, pdInfoBuilder, phyloseq, qrqc, QuasR, R453Plus1Toolbox, REDseq, Repitools, rGADEM, Rolexa, rSFFreader, rtracklayer, SeqArray, TFBSTools, VariantAnnotation, VariantTools
Suggests Me	annotate, BeadArrayUseCases, CSAR, exomeCopy, GenomicFeatures, GenomicRanges, genoset, methylumi, microRNA, MiRaGE, pcaGoPromoter, procoil, rTRM, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20110815, SNPlocs.Hsapiens.dbSNP.20111119, SNPlocs.Hsapiens.dbSNP.20120608, XVector

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	Biostrings_2.30.1.tar.gz
Windows Binary	Biostrings_2.30.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Biostrings_2.30.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats