ShortRead
This is the released version of ShortRead; for the devel version, see ShortRead.
FASTQ input and manipulation
Bioconductor version: Release (3.23)
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("ShortRead")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 1.70.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (18 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), 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 |
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, fraq, GOTHiC, icetea, IONiseR, metabinR, nucleR, posDemux, QuasR, R453Plus1Toolbox, RSVSim, scruff, UMI4Cats, seqpac, DBTC, genBaRcode, QsRutils, tidyGenR |
| Suggests Me | BiocParallel, CSAR, DspikeIn, GenomicAlignments, Rsamtools, S4Vectors, HiCDataLymphoblast, systemPipeRdata, yeastRNASeq, demulticoder, inDAGO, vectra |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ShortRead_1.70.0.tar.gz |
| Windows Binary (x86_64) | ShortRead_1.70.0.zip |
| macOS Binary (big-sur-x86_64) | ShortRead_1.70.0.tgz |
| macOS Binary (sonoma-arm64) | ShortRead_1.70.0.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 |