Biostrings

This is the released version of Biostrings; for the devel version, see Biostrings.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Efficient manipulation of biological strings

Bioconductor version: Release (3.23)

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], Wolfgang Huber [ctb] ('matchprobes' vignette), Beryl Kanali [ctb] (Converted 'MultipleAlignments' vignette from Sweave to RMarkdown), Haleema Khan [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Aidan Lakshman [ctb], Kieran O'Neill [ctb], Valerie Obenchain [ctb], Marcel Ramos [ctb], Albert Vill [ctb], Jen Wokaty [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Erik Wright [ctb]

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

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

Hervé Pagès, Patrick Aboyoun, Robert Gentleman, Saikat DebRoy. Biostrings: Efficient manipulation of biological strings. doi:10.18129/B9.bioc.Biostrings, R package version 2.80.2, https://bioconductor.org/packages/Biostrings.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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
Pairwise Sequence Alignments	PDF
Handling probe sequence information	HTML	R Script
Multiple Alignments	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version	2.80.2
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 years)
License	Artistic-2.0
Depends	R (>= 4.1.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), Seqinfo
Imports	methods, grDevices, stats, crayon
System Requirements
URL	https://bioconductor.org/packages/Biostrings
Bug Reports	https://github.com/Bioconductor/Biostrings/issues

Suggests	utils, graphics, pwalign, 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, BiocStyle, knitr, testthat (>= 3.0.0), covr
Linking To	S4Vectors, IRanges, XVector
Enhances
Depends On Me	alabaster.string, altcdfenvs, amplican, Basic4Cseq, BRAIN, BSgenome, BSgenomeForge, chimeraviz, ChIPanalyser, ChIPsim, cigarillo, CleanBSequences, cleaver, CODEX, CRISPRseek, DECIPHER, deepSNV, FDb.FANTOM4.promoters.hg19, GeneRegionScan, generegulation, GenomicAlignments, GOTHiC, harbChIP, HelloRanges, igblastr, JASPAR2014, kebabs, MethTargetedNGS, minfi, Modstrings, MotifDb, motifTestR, 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, pwalign, PWMEnrich, QSutils, queeems, R453Plus1Toolbox, R4RNA, rBLAST, REDseq, RiboProfiling, Rsamtools, RSVSim, rSWeeP, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, sequencing, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, SubVis, svaNUMT, systemPipeR, topdownr, transmogR, TreeSummarizedExperiment, triplex, VarCon
Imports Me	AbSolution, ActiveDriverWGS, alakazam, AllelicImbalance, AnnotationBustR, AnnotationHubData, AntibodyForests, appreci8R, AssessORF, ATACseqQC, BASiNET, BASiNETEntropy, BBCAnalyzer, BCRANK, bcSeq, BEAT, betterChromVAR, BgeeCall, BIGr, biomartr, biovizBase, branchpointer, bsseq, BUMHMM, BUSpaRse, CAGEr, CellBarcode, ChIPpeakAnno, ChIPseqR, ChIPsim, chromVAR, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, CleanUpRNAseq, cliProfiler, ClustIRR, CNEr, CNVfilteR, cogeqc, compEpiTools, copyseparator, coRdon, crisprBase, crisprBowtie, crisprDesign, crispRdesignR, crisprScore, crisprShiny, CrispRVariants, crisprViz, CSESA, cubar, customProDB, dada2, dagLogo, DAMEfinder, Damsel, decompTumor2Sig, diffHic, DiPALM, DMRcaller, DNAmotif, DNAshapeR, DominoEffect, DOTSeq, doubletrouble, DspikeIn, DuplexDiscovereR, easyRNASeq, EDASeq, eDNAfuns, enhancerHomologSearch, ensembldb, ensembleTax, epiSeeker, EpiSemble, EpiTxDb, esATAC, eudysbiome, EuPathDB, EventPointer, factR, FastqCleaner, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FLAMES, fRagmentomics, fraq, G4SNVHunter, GA4GHclient, GB5mcPred, gcapc, gcrma, gDNAx, genBaRcode, GencoDymo2, GeneRegionScan, GeneStructureTools, genomation, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, GenomicSig, GenVisR, geomeTriD, ggbio, ggmsa, gmapR, gmoviz, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCaptuRe, HiCDCPlus, HiCPotts, HiLDA, HiTC, icetea, idpr, iimi, immReferent, InPAS, IntEREst, IONiseR, ipdDb, IsoformSwitchAnalyzeR, KEGGREST, kmeRtone, LACHESIS, longreadvqs, LymphoSeq, m6Aboost, MatrixRider, MDTS, MEDIPS, MEDME, memes, MesKit, metabinR, metaCluster, MetaScope, metaseqR2, methimpute, methodical, methylPipe, methylscaper, mia, microbiome, microbiomeDataSets, MicrobiotaProcess, microRNA, MiscMetabar, MitoHEAR, MMDiff2, mobileRNA, monaLisa, Motif2Site, motifbreakR, motifcounter, motifmatchr, MotifPeeker, motifStack, MSA2dist, MSnID, MSstatsLiP, MSstatsPTM, multicrispr, MungeSumstats, musicatk, MutationalPatterns, MutSeqR, NanoMethViz, NanoStringNCTools, ngsReports, nucleR, oligoClasses, OmaDB, OpEnCAMeO, OpEnCAST, OpEnHiMR, openPrimeR, ORFik, OTUbase, packFinder, PACVr, 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, PICB, piglet, pipeFrame, planttfhunter, podkat, posDemux, postNet, primirTSS, proBAMr, ProbeDeveloper, procoil, profileplyr, ProteoDisco, PureCN, Pviz, qPLEXanalyzer, qsea, QsRutils, QuasR, r3Cseq, raer, ramwas, RCAS, Rcpi, recoup, refseqR, regioneR, regutools, REMP, RESOLVE, revert, rfaRm, rhinotypeR, RiboCrypt, ribosomeProfilingQC, RNAmodR, rprimer, Rqc, rtracklayer, sarks, SATS, scanMiR, scanMiRApp, scifer, scmeth, SCOPE, scoreInvHap, scoup, scPipe, scruff, SEMPLR, SeqArray, seqmagick, seqpac, seqPattern, SGSeq, signeR, SigsPack, sitadela, SNPhood, soGGi, SomaticSignatures, SparseSignatures, spiky, SpliceImpactR, SpliceWiz, SPLINTER, SQMtools, sscu, StructuralVariantAnnotation, supersigs, surfaltr, SVAlignR, svaRetro, SynExtend, SynMut, syntenet, systemPipeRdata, TAPseq, TENET, TFBSTools, tidyGenR, TmCalculator, transite, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, universalmotif, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, vhcub, VIProDesign, wavClusteR, YAPSA
Suggests Me	alabaster.files, annotate, AnnotationForge, AnnotationHub, autonomics, bambu, BANDITS, baseq, bbl, BeadArrayUseCases, bio3d, BOLDconnectR, BOLDNODE, CSAR, demulticoder, DNAcycP2, eisaR, file2meco, geneviewer, GenomicFiles, GenomicRanges, GenomicTuples, ggseqalign, ggtree, gkmSVM, gwas2crispr, GWASTools, HiContacts, HPiP, inDAGO, karyotapR, maftools, maGUI, methrix, methylumi, microbial, MiRaGE, mitoClone2, msaR, mutscan, NameNeedle, nuCpos, orthGS, phangorn, plyinteractions, polyRAD, protr, PTMods, RNAmodR.AlkAnilineSeq, rpx, rTRM, screenCounter, sigminer, Signac, 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, tidysq, treeio, tripr, vectra, ViralEntropR, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Links To Me	DECIPHER, kebabs, MatrixRider, posDemux, pwalign, Rsamtools, ShortRead, triplex, VariantAnnotation, VariantFiltering
Build Report	Build Report, r-universe

Package Archives

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

Source Package	Biostrings_2.80.2.tar.gz
Windows Binary (x86_64)	Biostrings_2.80.2.zip (64-bit only)
macOS Binary (big-sur-x86_64)	Biostrings_2.80.2.tgz
macOS Binary (sonoma-arm64)	Biostrings_2.80.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Biostrings
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Biostrings
Package Short Url	https://bioconductor.org/packages/Biostrings/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive