ShortRead

DOI: 10.18129/B9.bioc.ShortRead  

FASTQ input and manipulation

Bioconductor version: Release (3.16)

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: Bioconductor Package Maintainer [cre], Martin Morgan [aut], Michael Lawrence [ctb], Simon Anders [ctb]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ShortRead")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.56.1
In Bioconductor since	BioC 2.3 (R-2.8) (14.5 years)
License	Artistic-2.0
Depends	BiocGenerics(>= 0.23.3), BiocParallel, Biostrings(>= 2.47.6), Rsamtools(>= 1.31.2), GenomicAlignments(>= 1.15.6)
Imports	Biobase, S4Vectors(>= 0.17.25), IRanges(>= 2.13.12), GenomeInfoDb(>= 1.15.2), GenomicRanges(>= 1.31.8), hwriter, methods, zlibbioc, lattice, latticeExtra
LinkingTo	S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
Suggests	BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/ShortRead https://github.com/Bioconductor/ShortRead https://support.bioconductor.org/tag/ShortRead
BugReports	https://github.com/Bioconductor/ShortRead/issues
Depends On Me	chipseq, EatonEtAlChIPseq, EDASeq, esATAC, girafe, HTSeqGenie, NestLink, OTUbase, Rqc, segmentSeq, sequencing, systemPipeR
Imports Me	amplican, ArrayExpressHTS, basecallQC, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, MACPET, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, UMI4Cats
Suggests Me	BiocParallel, CSAR, FLAMES, GenomicAlignments, HiCDataLymphoblast, PING, Repitools, Rsamtools, S4Vectors, systemPipeRdata, yeastRNASeq
Links To Me
Build Report

Package Archives

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

Source Package	ShortRead_1.56.1.tar.gz
Windows Binary	ShortRead_1.56.1.zip
macOS Binary (x86_64)	ShortRead_1.56.1.tgz
macOS Binary (arm64)	ShortRead_1.56.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ShortRead
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ShortRead
Bioc Package Browser	https://code.bioconductor.org/browse/ShortRead/
Package Short Url	https://bioconductor.org/packages/ShortRead/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive