ShortRead

DOI: 10.18129/B9.bioc.ShortRead    

FASTQ input and manipulation

Bioconductor version: Release (3.6)

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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ShortRead")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ShortRead")

 

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

Details

biocViews	DataImport, QualityControl, Sequencing, Software
Version	1.36.1
In Bioconductor since	BioC 2.3 (R-2.8) (9.5 years)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.23.3), BiocParallel, Biostrings(>= 2.37.1), Rsamtools(>= 1.21.4), GenomicAlignments(>= 1.5.4)
Imports	Biobase, S4Vectors(>= 0.13.8), IRanges(>= 2.3.7), GenomeInfoDb(>= 1.1.19), GenomicRanges(>= 1.21.6), hwriter, methods, zlibbioc, lattice, latticeExtra
LinkingTo	S4Vectors, IRanges, XVector, Biostrings
Suggests	BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
SystemRequirements
Enhances
URL
Depends On Me	chipseq, EatonEtAlChIPseq, EDASeq, esATAC, girafe, HTSeqGenie, nucleR, OTUbase, Rqc, rSFFreader, segmentSeq, systemPipeR
Imports Me	amplican, ArrayExpressHTS, basecallQC, BEAT, chipseq, ChIPseqR, ChIPsim, dada2, easyRNASeq, GOTHiC, IONiseR, metagenomeFeatures, QuasR, R453Plus1Toolbox, RSVSim
Suggests Me	BiocParallel, CSAR, DBChIP, GenomicAlignments, Genominator, HiCDataLymphoblast, PICS, PING, Repitools, RnaSeqTutorial, Rsamtools, S4Vectors, yeastRNASeq
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ShortRead_1.36.1.tar.gz
Windows Binary	ShortRead_1.36.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	ShortRead_1.36.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ShortRead
Package Short Url	http://bioconductor.org/packages/ShortRead/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive