Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.6

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 Efficient genome searching with Biostrings and the BSgenome data packages
PDF R Script Handling probe sequence information
PDF R Script Pairwise Sequence Alignments
PDF R Script Some old notes about the vectorization feature of the DNAString() constructor. Not for the end user.
PDF   Reference Manual

Details

biocViews SequenceMatching, Genetics, Infrastructure
Depends R (>= 2.8.0), methods, IRanges(>= 1.6.6)
Imports graphics, methods, stats, utils, IRanges, Biobase
Suggests BSgenome(>= 1.13.14), BSgenome.Celegans.UCSC.ce2(>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.3.11), drosophila2probe, hgu95av2probe, GenomicFeatures(>= 0.1.3), hgu95av2cdf, affy, affydata(>= 1.11.5), RUnit
System Requirements
License Artistic-2.0
URL
Depends On Me altcdfenvs, BSgenome, ChIPpeakAnno, ChIPsim, GeneRegionScan, harbChIP, matchprobes, rGADEM, Rsamtools, ShortRead
Imports Me AffyCompatible, BCRANK, biocDatasets, BioSeqClass, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, gcrma, geneLenDataBase, GeneRegionScan, GenomicFeatures, girafe, MEDME, methVisual, microRNA, oligoClasses, 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.cytogenetics.array, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hg.u95a, pd.hg.u95av2, pd.ht.hg.u133.plus.pm, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pdInfoBuilder, rGADEM, Rolexa, Rsamtools, rtracklayer, ShortRead
Suggests Me annotate, microRNA, oneChannelGUI, SLGI, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427
Version 2.16.9
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source Biostrings_2.16.9.tar.gz
Windows Binary Biostrings_2.16.9.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Biostrings_2.16.9.tgz
Package Downloads Report Download Stats

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