Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/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 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 2.33.1
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(>= 1.21.35), XVector(>= 0.3.6)
Imports graphics, methods, stats, utils, BiocGenerics, IRanges, XVector, zlibbioc
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
System Requirements
URL
Depends On Me altcdfenvs, Basic4Cseq, BRAIN, BSgenome, ChIPpeakAnno, ChIPsim, cleaver, CRISPRseek, DASiR, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, GeneRegionScan, genomes, GenomicAlignments, GOTHiC, harbChIP, iPAC, JASPAR2014, methVisual, minfi, MotifDb, motifRG, oligo, oneChannelGUI, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ragene.2.0.st, pd.ragene.2.1.st, PWMEnrich, qrqc, R453Plus1Toolbox, REDseq, rGADEM, Roleswitch, Rsamtools, rSFFreader, RSVSim, sangerseqR, SCAN.UPC, scsR, seqbias, ShortRead, spliceSites, triplex, waveTiling
Imports Me AffyCompatible, AllelicImbalance, ArrayExpressHTS, BCRANK, BEAT, BioSeqClass, biovizBase, BSgenome, charm, ChIPseqR, ChIPsim, CNEr, cobindR, customProDB, dagLogo, easyRNASeq, ensemblVEP, gcrma, GeneRegionScan, GenomicAlignments, GenomicFeatures, ggbio, GGtools, girafe, gmapR, Gviz, gwascat, h5vc, HiTC, HTSeqGenie, KEGGREST, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, 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.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.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.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, Rcpi, REDseq, Repitools, rGADEM, Rolexa, rSFFreader, rtracklayer, SeqArray, SomaticSignatures, synapter, TFBSTools, VariantAnnotation, VariantFiltering, VariantTools
Suggests Me annotate, BeadArrayUseCases, CSAR, exomeCopy, 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, XVector

Package Downloads

Package Source Biostrings_2.33.1.tar.gz
Windows Binary Biostrings_2.33.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Biostrings_2.33.1.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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