ShortRead (original) (raw)
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, seeShortRead.
Classes and methods for high-throughput short-read sequencing data.
Bioconductor version: 2.12
Base classes, functions, and methods for representation of high-throughput, short-read sequencing data.
Author: Martin Morgan, Michael Lawrence, Simon Anders
Maintainer: Bioconductor Package Maintainer
Citation (from within R, enter citation("ShortRead")):
Installation
To install this package, start R and enter:
try http:// if https:// URLs are not supported
source("https://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 | |
|---|---|---|
| ShortRead_and_HilbertVis.pdf | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, HighThroughputSequencing, QualityControl, Sequencing, Software |
|---|---|
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.3 (R-2.8) (7.5 years) |
| License | Artistic-2.0 |
| Depends | methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.17.18), GenomicRanges(>= 1.11.18), Biostrings(>= 2.25.6), lattice, Rsamtools(>= 1.7.42), latticeExtra |
| Imports | BiocGenerics, IRanges, GenomicRanges, Biostrings, Biobase, hwriter, Rsamtools, zlibbioc, lattice |
| LinkingTo | IRanges, Biostrings |
| Suggests | biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi |
| SystemRequirements | |
| Enhances | Rmpi, parallel |
| URL | |
| Depends On Me | chipseq, ChIPseqR, easyRNASeq, EatonEtAlChIPseq, EDASeq, girafe, HTSeqGenie, nucleR, OTUbase, Rolexa, rSFFreader, segmentSeq |
| Imports Me | ArrayExpressHTS, chipseq, ChIPseqR, ChIPsim, nucleR, OTUbase, QuasR, R453Plus1Toolbox, Rolexa, rSFFreader, RSVSim |
| Suggests Me | CSAR, DBChIP, Genominator, PICS, PING, R453Plus1Toolbox, Repitools, RnaSeqTutorial, Rsamtools, yeastRNASeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ShortRead_1.18.0.tar.gz |
|---|---|
| Windows Binary | ShortRead_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ShortRead_1.18.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ShortRead/tree/release-2.12 |
| Package Short Url | http://bioconductor.org/packages/ShortRead/ |
| Package Downloads Report | Download Stats |