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Biostrings

Efficient manipulation of biological strings

Bioconductor version: Release (3.17)

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Author: Hervé Pagès [aut, cre], Patrick Aboyoun [aut], Robert Gentleman [aut], Saikat DebRoy [aut], Vince Carey [ctb], Nicolas Delhomme [ctb], Felix Ernst [ctb], Aidan Lakshman [ctb], Kieran O'Neill [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Albert Vill [ctb], Erik Wright [ctb]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

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

Details

biocViews Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version 2.68.1
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 18 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.31.2), XVector(>= 0.37.1), GenomeInfoDb
Imports methods, utils, grDevices, graphics, stats, crayon
Linking To 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
System Requirements
Enhances Rmpi
URL https://bioconductor.org/packages/Biostrings
Bug Reports https://github.com/Bioconductor/Biostrings/issues
See More
Depends On Me alabaster.string, altcdfenvs, amplican, Basic4Cseq, BRAIN, BSgenome, BSgenomeForge, chimeraviz, ChIPanalyser, ChIPsim, cleaver, CODEX, CRISPRseek, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, GeneRegionScan, generegulation, GenomicAlignments, GOTHiC, harbChIP, HelloRanges, hiReadsProcessor, iPAC, JASPAR2014, kebabs, MethTargetedNGS, minfi, Modstrings, MotifDb, msa, muscle, NestLink, oligo, ORFhunteR, 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.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, 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, periodicDNA, pqsfinder, PWMEnrich, qrqc, QSutils, R453Plus1Toolbox, R4RNA, REDseq, rGADEM, RiboProfiling, rRDP, Rsamtools, RSVSim, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, seqbias, sequencing, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, svaNUMT, systemPipeR, topdownr, TreeSummarizedExperiment, triplex, VarCon
Imports Me AllelicImbalance, alpine, AneuFinder, AnnotationHubData, appreci8R, ArrayExpressHTS, AssessORF, ATACseqQC, BBCAnalyzer, BCRANK, bcSeq, BEAT, BgeeCall, biovizBase, brainflowprobes, branchpointer, BSgenome, bsseq, BUMHMM, BUSpaRse, CellaRepertorium, CellBarcode, ChIPpeakAnno, ChIPseqR, ChIPsim, chromVAR, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, cliProfiler, CNEr, CNVfilteR, cogeqc, compEpiTools, consensusDE, coRdon, crisprBase, crisprBowtie, crisprDesign, crisprScore, CrispRVariants, crisprViz, customProDB, dada2, dagLogo, DAMEfinder, decompTumor2Sig, diffHic, DNAshapeR, DominoEffect, doubletrouble, easyRNASeq, EDASeq, enhancerHomologSearch, ensembldb, ensemblVEP, EpiTxDb, esATAC, eudysbiome, EuPathDB, EventPointer, exomePeak2, factR, FastqCleaner, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FLAMES, GA4GHclient, gcapc, gcrma, genbankr, GeneRegionScan, GeneStructureTools, genomation, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, GenVisR, ggbio, ggmsa, girafe, gmapR, gmoviz, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCDCPlus, HiLDA, HiTC, HTSeqGenie, icetea, idpr, IMMAN, InPAS, IntEREst, InterMineR, IONiseR, ipdDb, IsoformSwitchAnalyzeR, KEGGREST, LinTInd, LowMACA, LymphoSeq, m6Aboost, MADSEQ, MatrixRider, MDTS, MEDIPS, MEDME, memes, MesKit, MetaScope, metaseqR2, methimpute, methylPipe, methylscaper, mia, microbiome, microbiomeDataSets, microbiomeMarker, MicrobiotaProcess, microRNA, MMDiff2, monaLisa, Motif2Site, motifbreakR, motifcounter, motifmatchr, motifStack, MSA2dist, MSnID, MSstatsLiP, MSstatsPTM, multicrispr, MungeSumstats, musicatk, MutationalPatterns, NanoStringNCTools, ngsReports, nucleR, NxtIRFcore, oligoClasses, OmaDB, openPrimeR, ORFik, OTUbase, packFinder, 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, PhyloProfile, PhyloProfileData, phyloseq, pipeFrame, planttfhunter, podkat, polyester, primirTSS, proBAMr, procoil, ProteoDisco, PureCN, Pviz, qPLEXanalyzer, qrqc, qsea, QuasR, r3Cseq, ramwas, RCAS, Rcpi, recoup, regioneR, regutools, REMP, Repitools, RESOLVE, rfaRm, rGADEM, RiboCrypt, ribosomeProfilingQC, RNAmodR, rprimer, Rqc, rtracklayer, sarks, scanMiR, scanMiRApp, scifer, scmeth, SCOPE, scoreInvHap, scPipe, scruff, seqArchR, seqArchRplus, SeqArray, seqpac, seqPattern, SGSeq, signeR, SigsPack, single, SingleMoleculeFootprinting, sitadela, SNPhood, soGGi, SomaticSignatures, SparseSignatures, spiky, SpliceWiz, SPLINTER, sscu, StructuralVariantAnnotation, supersigs, surfaltr, svaRetro, synapter, SynExtend, SynMut, syntenet, systemPipeRdata, TAPseq, TarSeqQC, TFBSTools, transite, trena, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, universalmotif, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, wavClusteR, XNAString, YAPSA
Suggests Me annotate, AnnotationForge, AnnotationHub, bambu, BANDITS, BeadArrayUseCases, BiocGenerics, BRGenomics, CINdex, CSAR, eisaR, exomeCopy, GenomicFiles, GenomicRanges, GWASTools, HiContacts, HPiP, maftools, methrix, methylumi, MiRaGE, mitoClone2, nuCpos, RNAmodR.AlkAnilineSeq, rpx, rSWeeP, rTRM, screenCounter, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, spatzie, splatter, systemPipeTools, treeio, tripr, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Links To Me DECIPHER, kebabs, MatrixRider, Rsamtools, ShortRead, triplex, VariantAnnotation, VariantFiltering
Build Report  

Package Archives

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

Source Package Biostrings_2.68.1.tar.gz
Windows Binary Biostrings_2.68.1.zip (64-bit only)
macOS Binary (x86_64) Biostrings_2.68.1.tgz
macOS Binary (arm64) Biostrings_2.68.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/Biostrings
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Biostrings
Bioc Package Browser https://code.bioconductor.org/browse/Biostrings/
Package Short Url https://bioconductor.org/packages/Biostrings/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive