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

Bioconductor version: 2.8

Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.

Author: Martin Morgan, Michael Lawrence, Simon Anders

Maintainer: Biocore Team c/o BioC user list <bioconductor 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


biocViews DataImport, Sequencing, HighThroughputSequencing, QualityControl
Depends methods, IRanges(>= 1.10.2), GenomicRanges, Biostrings(>= 2.19.0), lattice, Rsamtools
Imports IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools
Suggests biomaRt, RUnit
System Requirements
License Artistic-2.0
Depends On Me chipseq, ChIPseqR, DEGseq, EatonEtAlChIPseq, girafe, OTUbase, Rolexa, segmentSeq
Imports Me ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, OTUbase, R453Plus1Toolbox, Rolexa
Suggests Me CSAR, Genominator, PICS, R453Plus1Toolbox, Rsamtools, yeastRNASeq
Version 1.10.4
Since Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source ShortRead_1.10.4.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary ShortRead_1.10.4.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:


Mailing Lists »

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

Fred Hutchinson Cancer Research Center