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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
In most cases, you don't need to download the package archive at all.
ShortRead
FASTQ input and manipulation
Bioconductor version: 2.14
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 (from within R,
enter citation("ShortRead")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ShortRead")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ShortRead")
| R Script | An introduction to ShortRead | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, QualityControl, Sequencing, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) |
| License | Artistic-2.0 |
| Depends | BiocGenerics(>= 0.1.0), BiocParallel, Biostrings(>= 2.31.14), Rsamtools(>= 1.13.1), GenomicAlignments(>= 0.99.6) |
| Imports | Biobase, GenomicRanges(>= 1.15.26), IRanges(>= 1.21.22), hwriter, methods, zlibbioc, lattice, latticeExtra |
| Suggests | BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi |
| System Requirements | |
| URL | |
| Depends On Me | Basic4Cseq, chipseq, ChIPseqR, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, rSFFreader, segmentSeq |
| Imports Me | ArrayExpressHTS, BEAT, chipseq, ChIPseqR, ChIPsim, easyRNASeq, GOTHiC, nucleR, OTUbase, QuasR, R453Plus1Toolbox, Rolexa, rSFFreader, RSVSim |
| Suggests Me | CSAR, DBChIP, Genominator, HiCDataLymphoblast, PICS, PING, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ShortRead_1.22.0.tar.gz |
| Windows Binary | ShortRead_1.22.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ShortRead_1.22.0.tgz |
| Mac OS X 10.9 (Mavericks) | ShortRead_1.22.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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