Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.8

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Author: H. Pages, P. Aboyoun, R. Gentleman, and S. DebRoy

Maintainer: H. Pages <hpages at fhcrc.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("Biostrings")

To cite this package in a publication, start R and enter:

    citation("Biostrings")

Documentation

PDF R Script A short presentation of the basic classes defined in Biostrings 2
PDF R Script Handling probe sequence information
PDF R Script Multiple Alignments
PDF R Script Pairwise Sequence Alignments
PDF   Reference Manual

Details

biocViews SequenceMatching, Genetics, Sequencing, Infrastructure, DataImport, DataRepresentation
Depends R (>= 2.8.0), methods, IRanges(>= 1.10.2)
Imports graphics, methods, stats, utils, IRanges
Suggests BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures(>= 1.3.14), hgu95av2cdf, affy, affydata(>= 1.11.5), RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me altcdfenvs, BSgenome, ChIPpeakAnno, ChIPsim, GeneRegionScan, harbChIP, R453Plus1Toolbox, rGADEM, Rsamtools, seqbias, ShortRead
Imports Me AffyCompatible, ArrayExpressHTS, BCRANK, BioSeqClass, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, gcrma, GeneRegionScan, GenomicFeatures, girafe, MEDIPS, MEDME, methVisual, microRNA, oligo, oligoClasses, OTUbase, 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.ag, pd.barley1, pd.bovine, pd.bsubtilis, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, 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.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, 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.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.rat230.2, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhesus, pd.rice, pd.rn.u34, pd.s.aureus, pd.soybean, 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.zebrafish, pdInfoBuilder, R453Plus1Toolbox, rGADEM, Rolexa, Rsamtools, rtracklayer, ShortRead
Suggests Me annotate, CSAR, GenomicFeatures, microRNA, oneChannelGUI, procoil, SLGI, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109
Version 2.20.4
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source Biostrings_2.20.4.tar.gz
Windows Binary Biostrings_2.20.4.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Biostrings_2.20.4.tgz
Package Downloads Report Download Stats

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