To install this package, start R and enter:

source("http://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 (3.1)

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:

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 Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version 2.36.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 10 years)
License Artistic-2.0
Depends R (>= 2.8.0), methods, BiocGenerics(>= 0.11.3), S4Vectors(>= 0.5.21), IRanges(>= 2.1.2), XVector(>= 0.7.3)
Imports graphics, methods, stats, utils, BiocGenerics, IRanges, XVector, zlibbioc
LinkingTo S4Vectors(>= 0.5.21), 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, LowMACA, MethTargetedNGS, methVisual, minfi, MotifDb, motifRG, motifStack, msa, muscle, oligo, oneChannelGUI, 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, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Roleswitch, rRDP, Rsamtools, RSVSim, sangerseqR, SCAN.UPC, scsR, SELEX, seqbias, ShortRead, spliceSites, ssviz, systemPipeR, triplex, waveTiling
Imports Me AffyCompatible, AllelicImbalance, ArrayExpressHTS, BCRANK, BEAT, BioSeqClass, biovizBase, BSgenome, charm, ChIPseqR, ChIPsim, CNEr, cobindR, compEpiTools, customProDB, dagLogo, diffHic, easyRNASeq, ensemblVEP, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FourCSeq, gcrma, GeneRegionScan, GenomicAlignments, GenomicFeatures, ggbio, GGtools, ggtree, girafe, gmapR, GoogleGenomics, Gviz, gwascat, h5vc, HiTC, HTSeqGenie, KEGGREST, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase3.release.v5a.20130502, MafDb.ESP6500SI.V2.SSA137, MafDb.ExAC.r0.3.sites, MatrixRider, MEDIPS, MEDME, methVisual, methylPipe, microRNA, 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, Pviz, qrqc, QuasR, r3Cseq, Rcpi, REDseq, Repitools, rGADEM, RNAprobR, Rolexa, Rqc, rSFFreader, rtracklayer, SeqArray, seqPattern, seqplots, SGSeq, soGGi, SomaticSignatures, synapter, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools, wavClusteR
Suggests Me annotate, BeadArrayUseCases, CSAR, exomeCopy, GenomicFiles, GenomicRanges, genoset, methylumi, microRNA, MiRaGE, pcaGoPromoter, 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, XVector
Build Report  

Package Archives

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

Package Source Biostrings_2.36.1.tar.gz
Windows Binary Biostrings_2.36.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Biostrings_2.36.1.tgz
Mac OS X 10.9 (Mavericks) Biostrings_2.36.1.tgz
Subversion source (username/password: readonly)
GitHub source https://github.com/Bioconductor-mirror/Biostrings/tree/release-3.1
Package Short Url http://bioconductor.org/packages/Biostrings/
Package Downloads Report Download Stats

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