Biostrings
Efficient manipulation of biological strings
Bioconductor version: 3.24 · Package version: 2.81.9
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| 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), Haleema Khan [ctb] (Converted 'matchprobes' vignette from Sweave to RMarkdown), Aidan Lakshman [ctb], Michael Lawrence [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] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/Biostrings |
| Bug Reports | https://github.com/Bioconductor/Biostrings/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/Biostrings/ |
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 2.81.9, https://bioconductor.org/packages/Biostrings.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- A short presentation of the basic classes defined in Biostrings 2
- Biostrings Quick Overview
- Using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment
- MultipleAlignment Objects
- Pairwise Sequence Alignments
- Sequence Searching and Matching with Biostrings
Download
Follow the installation instructions to use this package in your R session.
| Source package | Biostrings_2.81.9.tar.gz |
| Windows binary (x86_64) | Biostrings_2.81.9.zip |
| macOS binary (arm64) | Biostrings_2.81.9.tgz |
| macOS binary (x86_64) | Biostrings_2.81.9.tgz |
Dependencies
Depends: R (>= 4.1.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.47.5), XVector (>= 0.37.1), Seqinfo
Imports: methods, grDevices, stats, crayon
LinkingTo: S4Vectors, IRanges, XVector
Suggests: utils, graphics, pwalign, MultipleAlignment, 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
Reverse dependencies
Depends On Me (231): 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, MultipleAlignment, 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, rprimer, Rsamtools, RSVSim, rSWeeP, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, sequencing, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, SubVis, svaNUMT, systemPipeR, topdownr, transmogR, TreeSummarizedExperiment, triplex, VarCon
Imports Me (305): AbSolution, ActiveDriverWGS, alakazam, AllelicImbalance, AnnotationBustR, AnnotationHubData, AntibodyForests, appreci8R, AssessORF, ATACseqQC, BamScale, BASiNET, BASiNETEntropy, BBCAnalyzer, BCRANK, bcSeq, BEAT, betterChromVAR, BgeeCall, BIGr, biomartr, biovizBase, branchpointer, bsseq, BUMHMM, BUSpaRse, CAGEr, CellBarcode, CGRphylo2, 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, geneClusterPattern, GeneRegionScan, GeneStructureTools, genomation, GenomAutomorphism, GenomicDistributions, GenomicFeatures, GenomicScores, GenomicSig, GenVisR, geomeTriD, ggbio, ggmsa, gmapR, gmoviz, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCaptuRe, HiCDCPlus, HiCPotts, HiLDA, icetea, idpr, iimi, immReferent, InPAS, IntEREst, 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, 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, pepVet, 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, RBPEqBind, RBPSpecificity, RCAS, Rcpi, recoup, refseqR, regioneR, regutools, REMP, RESOLVE, revert, rfaRm, rhinotypeR, RiboCrypt, ribosomeProfilingQC, RNAmodR, Rqc, rtracklayer, sarks, SATS, scanMiR, scanMiRApp, scifer, scmeth, SCOPE, scoreInvHap, scoup, scPipe, scruff, SEMPLR, SeqArray, seqmagick, seqpac, seqPattern, SGSeq, signeR, SigsPack, sigvar, sitadela, SNPhood, SomaticSignatures, SparseSignatures, spiky, SpliceImpactR, SpliceWiz, SPLINTER, SQMtools, sscu, StructuralVariantAnnotation, 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 (72): 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, S4Cartographer, 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, splatter, splicelogic, systemPipeTools, tidysq, treeio, tripr, vectra, ViralEntropR, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector
Links To Me (10): DECIPHER, kebabs, MatrixRider, posDemux, pwalign, Rsamtools, ShortRead, triplex, VariantAnnotation, VariantFiltering