This is the development version of Biostrings; for the stable release version, see Biostrings.
Efficient manipulation of biological stringsBioconductor version: Development (3.22)
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, entercitation("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.
DocumentationTo 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 Details biocViews Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software Version 2.77.2 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20 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, 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 alabaster.string, altcdfenvs, amplican, Basic4Cseq, BRAIN, BSgenome, BSgenomeForge, chimeraviz, ChIPanalyser, ChIPsim, cleaver, CODEX, CRISPRseek, DECIPHER, deepSNV, GeneRegionScan, GenomicAlignments, GOTHiC, HelloRanges, hiReadsProcessor, igblastr, kebabs, MethTargetedNGS, minfi, Modstrings, MotifDb, motifTestR, msa, muscle, oligo, ORFhunteR, periodicDNA, pqsfinder, pwalign, PWMEnrich, QSutils, R453Plus1Toolbox, R4RNA, rBLAST, REDseq, RiboProfiling, rRDP, Rsamtools, RSVSim, rSWeeP, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, svaNUMT, systemPipeR, topdownr, transmogR, TreeSummarizedExperiment, triplex, VarCon, 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, SubVis Imports Me AllelicImbalance, AnnotationHubData, appreci8R, AssessORF, ATACseqQC, BBCAnalyzer, BCRANK, bcSeq, BEAT, BgeeCall, biovizBase, branchpointer, bsseq, BUMHMM, BUSpaRse, CAGEr, CellBarcode, ChIPpeakAnno, ChIPseqR, ChIPsim, chromVAR, circRNAprofiler, CircSeqAlignTk, cleanUpdTSeq, CleanUpRNAseq, cliProfiler, CNVfilteR, cogeqc, consensusDE, coRdon, crisprBase, crisprBowtie, crisprDesign, crisprScore, crisprShiny, CrispRVariants, crisprViz, customProDB, dada2, dagLogo, DAMEfinder, Damsel, decompTumor2Sig, diffHic, DNAshapeR, DominoEffect, doubletrouble, DuplexDiscovereR, easyRNASeq, EDASeq, enhancerHomologSearch, ensembldb, EpiTxDb, esATAC, eudysbiome, EventPointer, factR, FastqCleaner, FLAMES, G4SNVHunter, GA4GHclient, gcapc, gcrma, gDNAx, GeneRegionScan, genomation, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, GenVisR, geomeTriD, ggbio, ggmsa, gmapR, gmoviz, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiLDA, HiTC, icetea, idpr, IntEREst, IONiseR, ipdDb, IsoformSwitchAnalyzeR, KEGGREST, LinTInd, LymphoSeq, m6Aboost, MatrixRider, MDTS, MEDIPS, MEDME, memes, MesKit, metaseqR2, methimpute, methodical, methylPipe, methylscaper, mia, microbiome, MicrobiotaProcess, microRNA, MMDiff2, mobileRNA, monaLisa, Motif2Site, motifbreakR, motifcounter, motifmatchr, MotifPeeker, motifStack, MSA2dist, MSnID, MSstatsLiP, MSstatsPTM, multicrispr, MungeSumstats, musicatk, MutationalPatterns, NanoMethViz, NanoStringNCTools, ngsReports, nucleR, oligoClasses, OmaDB, ORFik, OTUbase, packFinder, pdInfoBuilder, PhyloProfile, phyloseq, PICB, pipeFrame, planttfhunter, podkat, primirTSS, proBAMr, procoil, ProteoDisco, PureCN, Pviz, qPLEXanalyzer, qsea, QuasR, r3Cseq, raer, ramwas, RCAS, Rcpi, recoup, regioneR, regutools, REMP, Repitools, RESOLVE, rfaRm, rhinotypeR, RiboCrypt, ribosomeProfilingQC, RNAmodR, rprimer, Rqc, rtracklayer, sarks, scanMiR, scanMiRApp, scifer, scmeth, SCOPE, scoreInvHap, scoup, scPipe, scruff, seqArchR, seqArchRplus, SeqArray, seqPattern, SGSeq, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, SNPhood, soGGi, SomaticSignatures, SparseSignatures, spiky, SpliceWiz, SPLINTER, sscu, StructuralVariantAnnotation, supersigs, surfaltr, svaRetro, SynExtend, SynMut, syntenet, TAPseq, TENET, TFBSTools, transite, tRNA, tRNAdbImport, tRNAscanImport, TVTB, txcutr, tximeta, Ularcirc, UMI4Cats, universalmotif, VariantAnnotation, VariantExperiment, VariantFiltering, VariantTools, wavClusteR, YAPSA, 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, AntibodyForests, BASiNET, BASiNETEntropy, BIGr, biomartr, copyseparator, crispRdesignR, CSESA, cubar, deepredeff, DNAmotif, dowser, ensembleTax, EpiSemble, GB5mcPred, genBaRcode, GencoDymo2, geneHapR, GenomicSig, hoardeR, ICAMS, iimi, inDAGO, kmeRtone, longreadvqs, metaCluster, MIC, MitoHEAR, MixviR, ogrdbstats, OpEnHiMR, PACVr, Platypus, refseqR, revert, SATS, seqmagick, SMITIDstruct, SQMtools, vhcub, VIProDesign Suggests Me alabaster.files, annotate, AnnotationForge, AnnotationHub, autonomics, bambu, BANDITS, CSAR, DNAcycP2, eisaR, GenomicFiles, GenomicRanges, GenomicTuples, ggseqalign, GWASTools, HiContacts, HPiP, maftools, methrix, methylumi, MiRaGE, mitoClone2, nuCpos, plyinteractions, RNAmodR.AlkAnilineSeq, rpx, rTRM, screenCounter, spatzie, splatter, systemPipeTools, treeio, tripr, XVector, 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, bbl, bio3d, DDPNA, demulticoder, file2meco, geneviewer, gkmSVM, karyotapR, maGUI, MARVEL, MiscMetabar, msaR, NameNeedle, orthGS, phangorn, polyRAD, protr, seqtrie, sigminer, Signac, tidysq Links To Me DECIPHER, kebabs, MatrixRider, pwalign, Rsamtools, ShortRead, triplex, VariantAnnotation, VariantFiltering Build Report Build Report Package 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