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 | R Script | |
| Biostrings Quick Overview | ||
| Handling probe sequence information | HTML | R Script |
| Multiple Alignments | HTML | R Script |
| Pairwise Sequence Alignments | ||
| Reference Manual | ||
| NEWS | Text |
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/ |
| Package Downloads Report | Download Stats |