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ShortRead

FASTQ input and manipulation


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
An introduction to ShortRead PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, QualityControl, Sequencing, Software
Version 1.60.0
In Bioconductor since BioC 2.3 (R-2.8) (15.5 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
System Requirements
URL https://bioconductor.org/packages/ShortRead https://github.com/Bioconductor/ShortRead https://support.bioconductor.org/tag/ShortRead
Bug Reports https://github.com/Bioconductor/ShortRead/issues
See More
Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
Linking To S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
Enhances
Depends On Me chipseq, EatonEtAlChIPseq, EDASeq, esATAC, girafe, HTSeqGenie, NestLink, OTUbase, Rqc, segmentSeq, sequencing, systemPipeR
Imports Me amplican, basecallQC, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, seqpac, UMI4Cats
Suggests Me BiocParallel, CSAR, FLAMES, GenomicAlignments, HiCDataLymphoblast, PING, Repitools, Rsamtools, S4Vectors, systemPipeRdata, yeastRNASeq
Links To Me
Build Report Build Report

Package Archives

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

Source Package ShortRead_1.60.0.tar.gz
Windows Binary ShortRead_1.60.0.zip
macOS Binary (x86_64) ShortRead_1.60.0.tgz
macOS Binary (arm64) ShortRead_1.60.0.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