Biostrings
This is the development version of Biostrings; for the stable release version, see Biostrings.
Efficient manipulation of biological strings
Bioconductor version: Development (3.23)
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 "4.6") 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 | 2.79.1 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 20.5 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 | altcdfenvs, Basic4Cseq, BRAIN, ChIPsim, cigarillo, cleaver, CODEX, DECIPHER, GeneRegionScan, GenomicAlignments, igblastr, kebabs, MethTargetedNGS, Modstrings, motifTestR, msa, muscle, oligo, pqsfinder, pwalign, PWMEnrich, QSutils, R4RNA, rBLAST, Rsamtools, RSVSim, rSWeeP, sangerseqR, SCAN.UPC, SELEX, ShortRead, SICtools, SimFFPE, ssviz, Structstrings, systemPipeR, topdownr, 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, CleanBSequences, SubVis |
| Imports Me | AssessORF, BCRANK, bcSeq, BUMHMM, CellBarcode, ChIPseqR, ChIPsim, cogeqc, coRdon, crisprBase, crisprScore, CrispRVariants, dada2, DNAshapeR, easyRNASeq, eudysbiome, FastqCleaner, gcrma, GeneRegionScan, GenomAutomorphism, GenomicAlignments, GenomicDistributions, GenomicScores, ggmsa, h5vc, heatmaps, idpr, IONiseR, ipdDb, KEGGREST, LymphoSeq, MDTS, MEDME, memes, MesKit, methimpute, methylscaper, microbiome, MicrobiotaProcess, microRNA, motifcounter, MSA2dist, MSnID, MSstatsLiP, MSstatsPTM, NanoStringNCTools, ngsReports, nucleR, oligoClasses, OmaDB, openPrimeR, OTUbase, packFinder, pdInfoBuilder, PhyloProfile, phyloseq, PICB, planttfhunter, procoil, ramwas, Rcpi, rfaRm, rhinotypeR, rprimer, sarks, scanMiR, scifer, scoup, seqPattern, sscu, supersigs, surfaltr, SynExtend, SynMut, syntenet, transite, tRNA, tRNAdbImport, universalmotif, 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, alakazam, AntibodyForests, BASiNET, BASiNETEntropy, BIGr, biomartr, copyseparator, crispRdesignR, CSESA, cubar, deepredeff, DNAmotif, dowser, eDNAfuns, ensembleTax, EpiSemble, GB5mcPred, genBaRcode, GencoDymo2, geneHapR, GenomicSig, hoardeR, ICAMS, iimi, kmeRtone, longreadvqs, metaCluster, MIC, MitoHEAR, MixviR, ogrdbstats, OpEnHiMR, PACVr, Platypus, refseqR, revert, SATS, seqmagick, SMITIDstruct, SQMtools, SVAlignR, vhcub, VIProDesign |
| Suggests Me | annotate, AnnotationForge, AnnotationHub, autonomics, BANDITS, CSAR, DNAcycP2, eisaR, GenomicRanges, GenomicTuples, ggseqalign, ggtree, GWASTools, HiContacts, maftools, mutscan, nuCpos, rpx, rTRM, screenCounter, 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, bbl, bio3d, BOLDconnectR, DDPNA, demulticoder, file2meco, geneviewer, gkmSVM, gwas2crispr, inDAGO, karyotapR, maGUI, MiscMetabar, msaR, NameNeedle, orthGS, phangorn, polyRAD, protr, sigminer, Signac, tidysq |
| Links To Me | DECIPHER, kebabs, pwalign, Rsamtools, ShortRead, triplex |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Biostrings_2.79.1.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 |