Biostrings

String objects representing biological sequences, and matching algorithms

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

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

To install this package, start R and enter:

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

Documentation

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	R Script
Reference Manual

Details

biocViews	SequenceMatching , Genetics , Infrastructure
Depends	R , methods , IRanges
Imports	graphics , methods , stats , utils , IRanges , Biobase
Suggests	BSgenome , BSgenome.Celegans.UCSC.ce2 , BSgenome.Dmelanogaster.UCSC.dm3 , drosophila2probe , hgu95av2probe , GenomicFeatures , hgu95av2cdf , affy , affydata , RUnit
System Requirements
License	Artistic-2.0
URL
Depends On Me	BSgenome , ChIPpeakAnno , ChIPsim , GGtools , GeneRegionScan , ShortRead , altcdfenvs , matchprobes , microRNA
Imports Me	AffyCompatible , BCRANK , BioSeqClass , ChIPpeakAnno , ChIPseqR , ChIPsim , GeneRegionScan , GenomicFeatures , MEDME , Rolexa , ShortRead , biocDatasets , gcrma , oligoClasses , pdInfoBuilder , rtracklayer
Suggests Me	SLGI , annotate , oneChannelGUI

Package Downloads

Package source	Biostrings_2.14.12.tar.gz
Windows binary	Biostrings_2.14.12.zip
MacOS X 10.4 (Tiger) binary	Biostrings_2.14.11.tgz
MacOS X 10.5 (Leopard) binary	Biostrings_2.14.12.tgz
Package Downloads Report	Downloads Stats