To install this package, start R and enter:

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

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

ShortRead

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

Bioconductor version: 2.13

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:

source("http://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 1.20.0
In Bioconductor since BioC 2.3 (R-2.8)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.19.34), GenomicRanges(>= 1.13.43), Biostrings(>= 2.29.18), lattice, Rsamtools(>= 1.13.1)
Imports Biobase, hwriter, zlibbioc, latticeExtra
Suggests biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
System Requirements
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

Package Archives

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

Package Source ShortRead_1.20.0.tar.gz
Windows Binary ShortRead_1.20.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ShortRead_1.20.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center