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

Bioconductor version: 2.13

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>

Citation (from within R, enter citation("ShortRead")):


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


biocViews DataImport, HighThroughputSequencing, QualityControl, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 2.3 (R-2.8)
License Artistic-2.0
Depends methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.19.34), GenomicRanges(>= 1.13.43), Biostrings(>= 2.29.18), lattice, Rsamtools(>= 1.13.1)
Imports Biobase, hwriter, zlibbioc, latticeExtra
Suggests biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
System Requirements
Depends On Me chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, rSFFreader, segmentSeq
Imports Me ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, nucleR, OTUbase, QuasR, R453Plus1Toolbox, Rolexa, rSFFreader, RSVSim
Suggests Me CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq

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Package Source ShortRead_1.20.0.tar.gz
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Mac OS X 10.6 (Snow Leopard) ShortRead_1.20.0.tgz
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