ShortRead

Classes and methods for high-throughput short-read sequencing data.

Bioconductor version: Release (2.12)

Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.

Author: Martin Morgan, Michael Lawrence, Simon Anders

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

To install this package, start R and enter:

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

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

    citation("ShortRead")

PDF	R Script	An introduction to ShortRead
PDF		ShortRead_and_HilbertVis.pdf
PDF		Reference Manual
Text		NEWS

biocViews	DataImport, HighThroughputSequencing, QualityControl, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 2.3 (R-2.8)
License	Artistic-2.0
Depends	methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.17.18), GenomicRanges(>= 1.11.18), Biostrings(>= 2.25.6), lattice, Rsamtools(>= 1.7.42), latticeExtra
Imports	BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice
Suggests	biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
System Requirements
URL
Depends On Me	chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, segmentSeq
Imports Me	ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, nucleR, OTUbase, QuasR, R453Plus1Toolbox, Rolexa, rSFFreader, RSVSim
Suggests Me	CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq

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