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")):

Installation

To install this package, start R and enter:

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

Documentation

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

Details

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  

Package Archives

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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