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

FASTQ input and manipulation

Bioconductor version: 3.0

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

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		Reference Manual
Text		NEWS

Details

biocViews	DataImport, QualityControl, Sequencing, Software
Version	1.24.0
In Bioconductor since	BioC 2.3 (R-2.8)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.11.3), BiocParallel, Biostrings(>= 2.33.14), Rsamtools(>= 1.17.28), GenomicAlignments(>= 1.1.28)
Imports	Biobase, S4Vectors(>= 0.2.2), IRanges(>= 1.99.27), GenomeInfoDb(>= 1.1.19), GenomicRanges(>= 1.17.39), hwriter, methods, zlibbioc, lattice, latticeExtra
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
Suggests	BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
SystemRequirements
Enhances
URL
Depends On Me	Basic4Cseq, chipseq, ChIPseqR, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, Rqc, rSFFreader, segmentSeq, systemPipeR
Imports Me	ArrayExpressHTS, BEAT, chipseq, ChIPseqR, ChIPsim, easyRNASeq, GOTHiC, nucleR, QuasR, R453Plus1Toolbox, Rolexa, RSVSim
Suggests Me	BiocParallel, CSAR, DBChIP, Genominator, HiCDataLymphoblast, PICS, PING, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq
Build Report

Package Archives

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

Package Source	ShortRead_1.24.0.tar.gz
Windows Binary	ShortRead_1.24.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	ShortRead_1.24.0.tgz
Mac OS X 10.9 (Mavericks)	ShortRead_1.24.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats

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