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

Bioconductor version: Release (2.11)

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>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



PDF R Script An introduction to ShortRead
PDF ShortRead_and_HilbertVis.pdf
PDF   Reference Manual
Text   NEWS


biocViews DataImport, HighThroughputSequencing, QualityControl, Sequencing, Software
Version 1.16.4
In Bioconductor since BioC 2.3 (R-2.8)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.13.4), GenomicRanges(>= 1.7.43), Biostrings(>= 2.25.6), lattice, Rsamtools(>= 1.7.42), latticeExtra
Imports BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice
Suggests biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
System Requirements
Depends On Me chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, segmentSeq
Imports Me ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, HiTC, nucleR, OTUbase, R453Plus1Toolbox, Rolexa, rSFFreader
Suggests Me CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq

Package Downloads

Package Source ShortRead_1.16.4.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) ShortRead_1.16.4.tgz
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