ShortRead
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ShortRead.
FASTQ input and manipulation
Bioconductor version: 3.9
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: Martin Morgan, Michael Lawrence, Simon Anders
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("ShortRead")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 1.42.0 |
| 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 |
See More
| Suggests | BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi |
| Linking To | S4Vectors, IRanges, XVector, Biostrings |
| Enhances | |
| Depends On Me | chipseq, EatonEtAlChIPseq, EDASeq, esATAC, girafe, HTSeqGenie, NestLink, OTUbase, Rqc, rSFFreader, segmentSeq, sequencing, systemPipeR |
| Imports Me | amplican, ArrayExpressHTS, basecallQC, BEAT, chipseq, ChIPseqR, ChIPsim, dada2, easyRNASeq, FastqCleaner, GOTHiC, icetea, IONiseR, MACPET, ngsReports, nucleR, QuasR, R453Plus1Toolbox, RSVSim, scruff |
| Suggests Me | BiocParallel, CSAR, DBChIP, GenomicAlignments, Genominator, HiCDataLymphoblast, PICS, PING, Repitools, Rsamtools, S4Vectors, yeastRNASeq |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ShortRead_1.42.0.tar.gz |
| Windows Binary | ShortRead_1.42.0.zip |
| Mac OS X 10.11 (El Capitan) | ShortRead_1.42.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |