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Bioconductor - ShortRead (development version)

ShortRead

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

FASTQ input and manipulation

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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")
Details biocViews DataImport, QualityControl, Sequencing, Software Version 1.67.0 In Bioconductor since BioC 2.3 (R-2.8) (16.5 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), 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 See More Suggests BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr Linking To S4Vectors, IRanges, XVector, Biostrings, Rhtslib Enhances Depends On Me chipseq, EDASeq, esATAC, OTUbase, Rqc, segmentSeq, systemPipeR, EatonEtAlChIPseq, NestLink, sequencing Imports Me amplican, basecallQC, BEAT, CellBarcode, chipseq, ChIPseqR, ChIPsim, CircSeqAlignTk, dada2, easyRNASeq, FastqCleaner, FLAMES, GOTHiC, icetea, IONiseR, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff, UMI4Cats, seqpac, DBTC, genBaRcode, inDAGO, rsahmi Suggests Me BiocParallel, CSAR, GenomicAlignments, Repitools, Rsamtools, S4Vectors, HiCDataLymphoblast, systemPipeRdata, yeastRNASeq, demulticoder Links To Me Build Report Build Report Package Archives

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


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