ShortRead
FASTQ input and manipulation
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") 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 | 1.62.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (16 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, 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, knitr |
| Linking To | S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc |
| Enhances | |
| Depends On Me | EDASeq, HTSeqGenie, OTUbase, Rqc, chipseq, esATAC, girafe, segmentSeq, systemPipeR, EatonEtAlChIPseq, NestLink, sequencing, STRMPS |
| Imports Me | BEAT, CellBarcode, ChIPseqR, ChIPsim, CircSeqAlignTk, FastqCleaner, GOTHiC, IONiseR, QuasR, R453Plus1Toolbox, RSVSim, UMI4Cats, amplican, basecallQC, chipseq, dada2, easyRNASeq, icetea, nucleR, scruff, seqpac, DBTC, genBaRcode |
| Suggests Me | BiocParallel, CSAR, FLAMES, GenomicAlignments, PING, Repitools, Rsamtools, S4Vectors, HiCDataLymphoblast, 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_1.62.0.tar.gz |
| Windows Binary (x86_64) | ShortRead_1.62.0.zip |
| macOS Binary (x86_64) | ShortRead_1.62.0.tgz |
| macOS Binary (arm64) | ShortRead_1.62.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ShortRead |
| Source Repository (Developer Access) | git clone [email protected]:packages/ShortRead |
| Bioc Package Browser | https://code.bioconductor.org/browse/ShortRead/ |
| Package Short Url | https://bioconductor.org/packages/ShortRead/ |
| Package Downloads Report | Download Stats |