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Biostrings

This is the development version of Biostrings; for the stable release version, see Biostrings.

Efficient manipulation of biological strings


Bioconductor version: Development (3.19)

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], 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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 HTML 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 2.71.2
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 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
System Requirements
URL https://bioconductor.org/packages/Biostrings
Bug Reports https://github.com/Bioconductor/Biostrings/issues
See More
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, BiocStyle, knitr
Linking To S4Vectors, IRanges, XVector
Enhances Rmpi
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, QSutils, R453Plus1Toolbox, R4RNA, REDseq, rGADEM, RiboProfiling, rRDP, Rsamtools, RSVSim, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, sequencing, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, svaNUMT, systemPipeR, topdownr, TreeSummarizedExperiment, triplex, VarCon
Imports Me AllelicImbalance, AneuFinder, AnnotationHubData, appreci8R, AssessORF, ATACseqQC, BBCAnalyzer, BCRANK, bcSeq, BEAT, BgeeCall, biovizBase, brainflowprobes, branchpointer, 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, gDNAx, 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, LymphoSeq, m6Aboost, MADSEQ, MatrixRider, MDTS, MEDIPS, MEDME, memes, MesKit, MetaScope, metaseqR2, methimpute, methodical, methylPipe, methylscaper, mia, microbiome, microbiomeDataSets, microbiomeMarker, MicrobiotaProcess, microRNA, MMDiff2, monaLisa, Motif2Site, motifbreakR, motifcounter, motifmatchr, motifStack, MSA2dist, MSnID, MSstatsLiP, MSstatsPTM, multicrispr, MungeSumstats, musicatk, MutationalPatterns, NanoMethViz, NanoStringNCTools, ngsReports, nucleR, 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, qsea, QuasR, r3Cseq, raer, 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, TFBSTools, transite, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, universalmotif, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, wavClusteR, XNAString, YAPSA
Suggests Me alabaster.files, annotate, AnnotationForge, AnnotationHub, bambu, BANDITS, BeadArrayUseCases, BiocGenerics, BRGenomics, CINdex, CSAR, eisaR, GenomicFiles, GenomicRanges, GenomicTuples, GWASTools, HiContacts, HPiP, maftools, methrix, methylumi, MiRaGE, mitoClone2, nuCpos, plyinteractions, 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 Build Report

Package Archives

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

Source Package Biostrings_2.71.2.tar.gz
Windows Binary Biostrings_2.71.2.zip
macOS Binary (x86_64) Biostrings_2.71.2.tgz
macOS Binary (arm64) Biostrings_2.71.1.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/
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