Biostrings

DOI: 10.18129/B9.bioc.Biostrings    

Efficient manipulation of biological strings

Bioconductor version: Release (3.14)

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

Author: H. Pagès, P. Aboyoun, R. Gentleman, and S. DebRoy

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

Installation

To install this package, start R (version "4.1") 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")

 

PDF	R Script	A short presentation of the basic classes defined in Biostrings 2
PDF		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	Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software
Version	2.62.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 17 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), XVector(>= 0.29.2), GenomeInfoDb
Imports	methods, utils, grDevices, graphics, stats, crayon
LinkingTo	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
SystemRequirements
Enhances	Rmpi
URL	https://bioconductor.org/packages/Biostrings
BugReports	https://github.com/Bioconductor/Biostrings/issues
Depends On Me	altcdfenvs, amplican, Basic4Cseq, BRAIN, BSgenome, 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, systemPipeR, topdownr, TreeSummarizedExperiment, triplex, VarCon
Imports Me	AffyCompatible, 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, cleanUpdTSeq, cliProfiler, CNEr, CNVfilteR, compEpiTools, consensusDE, coRdon, CrispRVariants, customProDB, dada2, dagLogo, DAMEfinder, decompTumor2Sig, diffHic, DNAshapeR, DominoEffect, easyRNASeq, EDASeq, enhancerHomologSearch, ensembldb, ensemblVEP, EpiTxDb, esATAC, eudysbiome, EuPathDB, EventPointer, exomePeak2, FastqCleaner, FDb.InfiniumMethylation.hg18, FDb.InfiniumMethylation.hg19, FindMyFriends, GA4GHclient, gcapc, gcrma, genbankr, GeneRegionScan, GeneStructureTools, GenoGAM, genomation, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, genphen, GenVisR, ggbio, ggmsa, girafe, gmapR, gmoviz, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCDCPlus, HiLDA, HiTC, HTSeqGenie, icetea, idpr, IMMAN, InPAS, IntEREst, InterMineR, IONiseR, ipdDb, IsoformSwitchAnalyzeR, KEGGREST, LowMACA, LymphoSeq, m6Aboost, MACPET, MADSEQ, MatrixRider, MDTS, MEDIPS, MEDME, memes, MesKit, metaseqR2, methimpute, methylPipe, methylscaper, mia, microbiomeDataSets, microbiomeMarker, MicrobiotaProcess, microRNA, MMDiff2, monaLisa, motifbreakR, motifcounter, motifmatchr, motifStack, 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, podkat, polyester, primirTSS, proBAMr, procoil, ProteoDisco, ProteomicsAnnotationHubData, PureCN, Pviz, qPLEXanalyzer, qrqc, qsea, QuasR, r3Cseq, ramwas, RCAS, Rcpi, recoup, regioneR, regutools, REMP, Repitools, rfaRm, rGADEM, RiboCrypt, ribosomeProfilingQC, RNAmodR, RNASeqR, Rqc, rtracklayer, sarks, scanMiR, scanMiRApp, scmeth, SCOPE, scoreInvHap, scruff, SeqArray, seqcombo, seqPattern, SGSeq, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, SNPhood, soGGi, SomaticSignatures, SparseSignatures, spiky, SPLINTER, sscu, StructuralVariantAnnotation, supersigs, surfaltr, svaNUMT, svaRetro, synapter, SynExtend, SynMut, TAPseq, TarSeqQC, TFBSTools, transite, trena, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, universalmotif, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, wavClusteR, XCIR, XNAString, YAPSA
Suggests Me	annotate, AnnotationForge, AnnotationHub, bambu, BANDITS, BeadArrayUseCases, BiocGenerics, BRGenomics, CINdex, CSAR, eisaR, exomeCopy, GenomicFiles, GenomicRanges, GWASTools, HPiP, maftools, methrix, methylumi, MiRaGE, mitoClone2, nuCpos, RNAmodR.AlkAnilineSeq, rpx, rSWeeP, rTRM, SNPlocs.Hsapiens.dbSNP.20101109, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.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_2.62.0.tar.gz
Windows Binary	Biostrings_2.62.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	Biostrings_2.62.0.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 3.14	Source Archive