To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")

In most cases, you don't need to download the package archive at all.

Biostrings

 

String objects representing biological sequences, and matching algorithms

Bioconductor version: Release (3.2)

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 fredhutch.org>

Citation (from within R, enter citation("Biostrings")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://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 A short presentation of the basic classes defined in Biostrings 2
PDF Biostrings Quick Overview
PDF Handling probe sequence information
PDF Multiple Alignments
PDF Pairwise Sequence Alignments
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version 2.38.4
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10.5 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.15.6), S4Vectors(>= 0.7.1), IRanges(>= 2.4.7), XVector(>= 0.9.3)
Imports graphics, methods, stats, utils, BiocGenerics, IRanges, XVector
LinkingTo S4Vectors, 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(>= 1.41.3), affydata(>= 1.11.5), RUnit
SystemRequirements
Enhances Rmpi
URL
Depends On Me altcdfenvs, Basic4Cseq, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, cleaver, CRISPRseek, DASiR, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, GeneRegionScan, genomes, GenomicAlignments, GOTHiC, harbChIP, hiReadsProcessor, iPAC, JASPAR2014, kebabs, MethTargetedNGS, methVisual, minfi, MotifDb, motifRG, motifStack, msa, muscle, oligo, oneChannelGUI, pcaGoPromoter, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, 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.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, 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.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, 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.hta.2.0, 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.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, 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.4.0, 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.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, 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.rabgene.1.0.st, pd.rabgene.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.1.0.st, 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.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, 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, PGA, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, RiboProfiling, Roleswitch, rRDP, Rsamtools, RSVSim, sangerseqR, SCAN.UPC, scsR, SELEX, seqbias, ShortRead, SICtools, spliceSites, ssviz, systemPipeR, triplex, waveTiling
Imports Me AffyCompatible, AllelicImbalance, AnnotationHubData, ArrayExpressHTS, BCRANK, BEAT, BioSeqClass, biovizBase, BSgenome, charm, ChIPseqR, ChIPsim, CNEr, cobindR, compEpiTools, customProDB, dagLogo, diffHic, easyRNASeq, EDASeq, ensemblVEP, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FindMyFriends, FourCSeq, gcrma, GeneRegionScan, genomation, GenomicAlignments, GenomicFeatures, ggbio, GGtools, ggtree, girafe, gmapR, GoogleGenomics, GUIDEseq, Gviz, gwascat, h5vc, HiTC, HTSeqGenie, IONiseR, KEGGREST, LowMACA, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ALL.wgs.phase3.release.v5b.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, MatrixRider, MEDIPS, MEDME, metagenomeFeatures, methVisual, methylPipe, microRNA, motifbreakR, motifRG, MotIV, oligoClasses, OTUbase, Pbase, 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.atdschip.tiling, pd.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, pdInfoBuilder, phyloseq, podkat, polyester, proBAMr, ProteomicsAnnotationHubData, Pviz, qrqc, QuasR, r3Cseq, Rcpi, REDseq, Repitools, rGADEM, RNAprobR, Rolexa, Rqc, rSFFreader, rtracklayer, SeqArray, seqPattern, seqplots, SGSeq, SNPhood, soGGi, SomaticSignatures, synapter, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR
Suggests Me annotate, AnnotationHub, BeadArrayUseCases, CSAR, exomeCopy, GenomicFiles, GenomicRanges, genoset, methylumi, microRNA, MiRaGE, procoil, rpx, 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, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Build Report  

Package Archives

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

Package Source Biostrings_2.38.4.tar.gz
Windows Binary Biostrings_2.38.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Biostrings_2.38.0.tgz
Mac OS X 10.9 (Mavericks) Biostrings_2.38.4.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/Biostrings/tree/release-3.2
Package Short Url http://bioconductor.org/packages/Biostrings/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center