Biostrings
Efficient manipulation of biological strings
Bioconductor version: 3.23 · Package version: 2.80.1
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), 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] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/Biostrings |
| Bug Reports | https://github.com/Bioconductor/Biostrings/issues |
| Downloads rank | 55189 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, DataImport, DataRepresentation, Genetics, Infrastructure, SequenceMatching, Sequencing, Software |
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
Download
Dependencies
Depends: R (>= 4.1.0), BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.31.2), XVector (>= 0.37.1), Seqinfo
Imports: methods, grDevices, stats, crayon
LinkingTo: S4Vectors, IRanges, XVector
Suggests: utils, 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
Reverse dependencies
Depends On Me (230): 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, 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, RiboProfiling, Rsamtools, RSVSim, rSWeeP, sangeranalyseR, sangerseqR, SCAN.UPC, SELEX, sequencing, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, SubVis, svaNUMT, systemPipeR, topdownr, transmogR, TreeSummarizedExperiment, triplex, VarCon
Imports Me (304): AbSolution, ActiveDriverWGS, alakazam, AllelicImbalance, AnnotationHubData, AntibodyForests, appreci8R, AssessORF, ATACseqQC, BASiNET, BASiNETEntropy, BBCAnalyzer, BCRANK, bcSeq, BEAT, betterChromVAR, BgeeCall, BIGr, biomartr, biovizBase, branchpointer, bsseq, BUMHMM, BUSpaRse, CAGEr, CellBarcode, 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, GeneRegionScan, GeneStructureTools, genomation, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicFeatures, GenomicScores, GenomicSig, GenVisR, geomeTriD, ggbio, ggmsa, gmapR, gmoviz, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCaptuRe, HiCDCPlus, HiCPotts, HiLDA, HiTC, icetea, idpr, iimi, immReferent, InPAS, IntEREst, IONiseR, 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, motifcounter, 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, 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, RCAS, Rcpi, recoup, refseqR, regioneR, regutools, REMP, RESOLVE, revert, rfaRm, rhinotypeR, RiboCrypt, ribosomeProfilingQC, RNAmodR, rprimer, Rqc, rtracklayer, sarks, SATS, scanMiR, scanMiRApp, scifer, scmeth, SCOPE, scoreInvHap, scoup, scPipe, scruff, SEMPLR, SeqArray, seqmagick, seqpac, seqPattern, SGSeq, signeR, SigsPack, sitadela, SNPhood, soGGi, SomaticSignatures, SparseSignatures, spiky, SpliceImpactR, SpliceWiz, SPLINTER, SQMtools, sscu, StructuralVariantAnnotation, supersigs, 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 (70): alabaster.files, annotate, AnnotationForge, AnnotationHub, autonomics, bambu, BANDITS, baseq, bbl, BeadArrayUseCases, bio3d, BOLDconnectR, 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, 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, spatzie, splatter, 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