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 3.2 of Bioconductor; for the stable, up-to-date release version, see ShortRead.

FASTQ input and manipulation

Bioconductor version: 3.2

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:

## 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 An introduction to ShortRead
PDF Reference Manual
Text NEWS

Details

biocViews DataImport, QualityControl, Sequencing, Software
Version 1.28.0
In Bioconductor since BioC 2.3 (R-2.8) (7.5 years)
License Artistic-2.0
Depends BiocGenerics(>= 0.11.3), BiocParallel, Biostrings(>= 2.37.1), Rsamtools(>= 1.21.4), GenomicAlignments(>= 1.5.4)
Imports Biobase, S4Vectors(>= 0.7.1), IRanges(>= 2.3.7), GenomeInfoDb(>= 1.1.19), GenomicRanges(>= 1.21.6), hwriter, methods, zlibbioc, lattice, latticeExtra
LinkingTo S4Vectors, IRanges, XVector, Biostrings
Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
SystemRequirements
Enhances
URL
Depends On Me chipseq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, Rqc, rSFFreader, segmentSeq, systemPipeR
Imports Me ArrayExpressHTS, BEAT, chipseq, ChIPseqR, ChIPsim, easyRNASeq, GOTHiC, IONiseR, metagenomeFeatures, QuasR, R453Plus1Toolbox, Rolexa, RSVSim
Suggests Me BiocParallel, CSAR, DBChIP, GenomicAlignments, 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_1.28.0.tar.gz
Windows Binary ShortRead_1.28.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ShortRead_1.28.0.tgz
Mac OS X 10.9 (Mavericks) ShortRead_1.28.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ShortRead/tree/release-3.2
Package Short Url http://bioconductor.org/packages/ShortRead/
Package Downloads Report Download Stats

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