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

Bioconductor version: 2.10

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>

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


biocViews DataImport, HighThroughputSequencing, QualityControl, Sequencing, Software
Depends methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.13.4), GenomicRanges(>= 1.7.43), Biostrings(>= 2.23.2), lattice, Rsamtools(>= 1.7.42), latticeExtra
Imports BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice
Suggests biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
System Requirements
License Artistic-2.0
Depends On Me chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, nucleR, OTUbase, Rolexa, segmentSeq
Imports Me ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, HiTC, nucleR, OTUbase, R453Plus1Toolbox, Rolexa
Suggests Me CSAR, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq
Version 1.14.4
Since Bioconductor 2.3 (R-2.8)

Package Downloads

Package Source ShortRead_1.14.4.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary ShortRead_1.14.4.tgz
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