ShortRead
This is thereleased version of ShortRead; for the devel version, seeShortRead.
FASTQ input and manipulation
Bioconductor version: Release (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("ShortRead")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("ShortRead")For older versions of R, please refer to the appropriateBioconductor 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 | 1.68.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (17 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/ShortReadhttps://github.com/Bioconductor/ShortReadhttps://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,RSVSim,scruff,UMI4Cats,seqpac,DBTC,genBaRcode,rsahmi |
| Suggests Me | BiocParallel,CSAR,DspikeIn,GenomicAlignments,Rsamtools,S4Vectors,HiCDataLymphoblast,systemPipeRdata,yeastRNASeq,demulticoder,inDAGO |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | ShortRead_1.68.0.tar.gz |
| Windows Binary (x86_64) | ShortRead_1.68.0.zip |
| macOS Binary (x86_64) | ShortRead_1.68.0.tgz |
| macOS Binary (arm64) | ShortRead_1.68.0.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 |