Biostrings

String objects representing biological sequences, and matching algorithms

Bioconductor version: 2.7

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 Multiple Alignments

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(>= 1.7.23)

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, R453Plus1Toolbox, rGADEM, Rsamtools, ShortRead

Imports Me AffyCompatible, BCRANK, biocDatasets, BioSeqClass, charm, ChIPpeakAnno, ChIPseqR, ChIPsim, gcrma, geneLenDataBase, GeneRegionScan, GenomicFeatures, girafe, MEDIPS, MEDME, methVisual, microRNA, oligoClasses, OTUbase, pd.081229.hg18.promoter.medip.hx1, pd.2006年07月18日.hg18.refseq.promoter, pd.2006年07月18日.mm8.refseq.promoter, pd.2006年10月31日.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, R453Plus1Toolbox, rGADEM, Rolexa, Rsamtools, rtracklayer, ShortRead

Suggests Me annotate, CSAR, GenomicFeatures, microRNA, oneChannelGUI, SLGI, SNPlocs.Hsapiens.dbSNP.20090506, SNPlocs.Hsapiens.dbSNP.20100427, SNPlocs.Hsapiens.dbSNP.20101109

Version 2.18.4

Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source Biostrings_2.18.4.tar.gz

Windows Binary Biostrings_2.18.4.zip (32- & 64-bit)

MacOS 10.5 (Leopard) binary Biostrings_2.18.4.tgz

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