ShortRead

This is the development version of ShortRead; for the stable release version, see ShortRead.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

FASTQ input and manipulation

Bioconductor version: Development (3.24)

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], Rohit Satyam [ctb] (Converted Overview.Rnw vignette from Sweave to RMarkdown / HTML.), J Wokaty [ctb]

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

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

Martin Morgan. ShortRead: FASTQ input and manipulation. doi:10.18129/B9.bioc.ShortRead, R package version 1.71.1, https://bioconductor.org/packages/ShortRead.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, QualityControl, Sequencing, Software
Version	1.71.1
In Bioconductor since	BioC 2.3 (R-2.8) (18 years)
License	Artistic-2.0
Depends	BiocGenerics (>= 0.59.9), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
Imports	Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, 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

Suggests	BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr
Linking To	S4Vectors, IRanges, XVector, Biostrings, Rhtslib
Enhances
Depends On Me	chipseq, EatonEtAlChIPseq, EDASeq, esATAC, NestLink, OTUbase, Rqc, segmentSeq, sequencing, systemPipeR
Imports Me	amplican, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, DBTC, easyRNASeq, FastqCleaner, FLAMES, genBaRcode, GOTHiC, icetea, metabinR, nucleR, posDemux, QsRutils, QuasR, R453Plus1Toolbox, RSVSim, scruff, seqpac, tidyGenR, UMI4Cats
Suggests Me	BiocParallel, CSAR, demulticoder, DspikeIn, fraq, GenomicAlignments, HiCDataLymphoblast, inDAGO, Rsamtools, S4Vectors, systemPipeRdata, vectra, yeastRNASeq
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ShortRead_1.71.1.tar.gz
Windows Binary (x86_64)	ShortRead_1.71.1.zip
macOS Binary (big-sur-x86_64)	ShortRead_1.71.1.tgz
macOS Binary (sonoma-arm64)	ShortRead_1.71.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ShortRead
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ShortRead
Package Short Url	https://bioconductor.org/packages/ShortRead/
Package Downloads Report	Download Stats