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
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