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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 (3.21)

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")):

Installation

To install this package, start R (version "4.5") 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 HTML R Script
Pairwise Sequence Alignments PDF
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 2.75.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.31.2), XVector(>= 0.37.1), GenomeInfoDb
Imports methods, utils, grDevices, stats, crayon
System Requirements
URL https://bioconductor.org/packages/Biostrings
Bug Reports https://github.com/Bioconductor/Biostrings/issues
See More
Suggests 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 BRAIN, BSgenomeForge, BSgenome, Basic4Cseq, CODEX, CRISPRseek, ChIPanalyser, ChIPsim, DECIPHER, GOTHiC, GeneRegionScan, GenomicAlignments, HelloRanges, MethTargetedNGS, Modstrings, MotifDb, ORFhunteR, PWMEnrich, QSutils, R453Plus1Toolbox, R4RNA, REDseq, RSVSim, RiboProfiling, Rsamtools, SCAN.UPC, SELEX, SICtools, ShortRead, SimFFPE, Structstrings, TreeSummarizedExperiment, VarCon, alabaster.string, altcdfenvs, amplican, chimeraviz, cleaver, deepSNV, hiReadsProcessor, kebabs, minfi, motifTestR, msa, muscle, oligo, periodicDNA, pqsfinder, pwalign, rBLAST, rGADEM, rRDP, rSWeeP, sangeranalyseR, sangerseqR, ssviz, svaNUMT, systemPipeR, transmogR, triplex, FDb.FANTOM4.promoters.hg19, 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, harbChIP, JASPAR2014, NestLink, generegulation, sequencing, CleanBSequences, STRMPS, SubVis
Imports Me ATACseqQC, AllelicImbalance, AneuFinder, AnnotationHubData, BBCAnalyzer, BCRANK, BEAT, BUMHMM, BUSpaRse, BgeeCall, CAGEr, CNEr, CNVfilteR, CellBarcode, ChIPpeakAnno, ChIPseqR, ChIPsim, CircSeqAlignTk, CleanUpRNAseq, CrispRVariants, DAMEfinder, DNAshapeR, Damsel, DominoEffect, DuplexDiscovereR, EDASeq, EpiTxDb, EventPointer, FLAMES, FastqCleaner, GA4GHclient, GRaNIE, GUIDEseq, GenVisR, GeneRegionScan, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, Gviz, HiLDA, HiTC, IONiseR, IntEREst, IsoformSwitchAnalyzeR, KEGGREST, LinTInd, LymphoSeq, MADSEQ, MDTS, MEDIPS, MEDME, MMDiff2, MSA2dist, MatrixRider, MesKit, MicrobiotaProcess, Motif2Site, MungeSumstats, MutationalPatterns, NanoMethViz, NanoStringNCTools, ORFik, OTUbase, OmaDB, PhyloProfile, ProteoDisco, PureCN, Pviz, QuasR, RCAS, REMP, RESOLVE, RNAmodR, Rcpi, Repitools, RiboCrypt, Rqc, SCOPE, SGSeq, SNPhood, SPLINTER, SeqArray, SigsPack, SingleMoleculeFootprinting, SomaticSignatures, SparseSignatures, SpliceWiz, StructuralVariantAnnotation, SynExtend, SynMut, TAPseq, TFBSTools, TVTB, UMI4Cats, Ularcirc, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, XNAString, YAPSA, appreci8R, bcSeq, biovizBase, branchpointer, bsseq, chromVAR, circRNAprofiler, cleanUpdTSeq, cliProfiler, coRdon, cogeqc, compEpiTools, consensusDE, crisprBase, crisprBowtie, crisprDesign, crisprScore, crisprShiny, crisprViz, customProDB, dada2, dagLogo, decompTumor2Sig, diffHic, doubletrouble, easyRNASeq, enhancerHomologSearch, ensembldb, esATAC, eudysbiome, factR, gDNAx, gcapc, gcrma, genomation, ggbio, ggmsa, girafe, gmapR, gmoviz, gwascat, h5vc, heatmaps, icetea, idpr, ipdDb, m6Aboost, memes, metaseqR2, methimpute, methylPipe, methylscaper, mia, microRNA, microbiome, mobileRNA, monaLisa, motifStack, motifbreakR, motifcounter, motifmatchr, multicrispr, musicatk, ngsReports, nucleR, oligoClasses, openPrimeR, packFinder, pdInfoBuilder, phyloseq, pipeFrame, planttfhunter, podkat, primirTSS, proBAMr, procoil, qsea, r3Cseq, rGADEM, raer, ramwas, recoup, regioneR, regutools, rfaRm, rhinotypeR, ribosomeProfilingQC, rprimer, rtracklayer, sarks, scPipe, scanMiRApp, scanMiR, scifer, scmeth, scoreInvHap, scoup, scruff, seqPattern, signeR, sitadela, soGGi, spiky, sscu, supersigs, surfaltr, svaRetro, syntenet, tRNA, tRNAdbImport, tRNAscanImport, transite, txcutr, tximeta, universalmotif, wavClusteR, EuPathDB, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, 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.charm.hg18.example, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.mirna.3.1, MetaScope, microbiomeDataSets, pd.atdschip.tiling, PhyloProfileData, systemPipeRdata, seqpac, alakazam, BASiNET, BASiNETEntropy, biomartr, copyseparator, crispRdesignR, CSESA, cubar, deepredeff, DNAmotif, dowser, EncDNA, ensembleTax, EpiSemble, GB5mcPred, genBaRcode, geneHapR, GenomicSig, hoardeR, ICAMS, iimi, immuneSIM, kibior, kmeRs, kmeRtone, longreadvqs, metaCluster, MicroSEC, MitoHEAR, MixviR, ogrdbstats, OpEnHiMR, PACVr, Platypus, PredCRG, refseqR, revert, SeedMatchR, seqmagick, simMP, SMITIDstruct, vhcub
Suggests Me AnnotationForge, AnnotationHub, BANDITS, CSAR, GWASTools, GenomicFiles, GenomicRanges, GenomicTuples, HPiP, HiContacts, MiRaGE, RNAmodR.AlkAnilineSeq, XVector, alabaster.files, annotate, autonomics, bambu, eisaR, ggseqalign, maftools, methrix, methylumi, mitoClone2, nuCpos, plyinteractions, rTRM, rpx, screenCounter, spatzie, splatter, systemPipeTools, treeio, tripr, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, BeadArrayUseCases, AhoCorasickTrie, bbl, bio3d, DDPNA, file2meco, gkmSVM, karyotapR, maGUI, MARVEL, MiscMetabar, msaR, NameNeedle, orthGS, phangorn, polyRAD, protr, seqtrie, sigminer, Signac, tidysq
Links To Me DECIPHER, MatrixRider, Rsamtools, ShortRead, VariantAnnotation, VariantFiltering, kebabs, pwalign, triplex
Build Report Build Report

Package Archives

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

Source Package Biostrings_2.75.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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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