To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ShortRead")

In most cases, you don't need to download the package archive at all.

ShortRead

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ShortRead.

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

Bioconductor version: 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>

Citation (from within R, enter citation("ShortRead")):

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ShortRead")

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("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) (7.5 years)
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
LinkingTo	IRanges, Biostrings
Suggests	biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
SystemRequirements
Enhances	Rmpi, parallel
URL
Depends On Me	chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, rSFFreader, 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
Build Report

Follow Installation instructions to use this package in your R session.

Package Source	ShortRead_1.18.0.tar.gz
Windows Binary	ShortRead_1.18.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ShortRead_1.18.0.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/ShortRead/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/ShortRead/
Package Downloads Report	Download Stats

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