ShortRead

FASTQ input and manipulation

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("ShortRead")

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

    citation("ShortRead")

Documentation

PDF R Script An introduction to ShortRead
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, QualityControl, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 2.3 (R-2.8)
License Artistic-2.0
Depends BiocGenerics(>= 0.1.0), BiocParallel, Biostrings(>= 2.31.14), Rsamtools(>= 1.13.1), GenomicAlignments(>= 0.99.6)
Imports Biobase, GenomicRanges(>= 1.15.26), IRanges(>= 1.21.22), hwriter, methods, zlibbioc, lattice, latticeExtra
Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
System Requirements
URL
Depends On Me Basic4Cseq, chipseq, ChIPseqR, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, rSFFreader, segmentSeq
Imports Me ArrayExpressHTS, BEAT, chipseq, ChIPseqR, ChIPsim, easyRNASeq, GOTHiC, nucleR, OTUbase, QuasR, R453Plus1Toolbox, Rolexa, rSFFreader, RSVSim
Suggests Me CSAR, DBChIP, Genominator, HiCDataLymphoblast, PICS, PING, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq

Package Downloads

Package Source ShortRead_1.23.0.tar.gz
Windows Binary ShortRead_1.23.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ShortRead_1.23.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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