ShortRead
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see ShortRead.
FASTQ input and manipulation
Bioconductor version: 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("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 | R Script | |
| Reference Manual | ||
| 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 (64-bit only) |
| 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 |