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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
In most cases, you don't need to download the package archive at all.
Rsamtools
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see Rsamtools.
Import aligned BAM file format sequences into R / Bioconductor
Bioconductor version: 2.8
This package provides an interface to the 'samtools' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map) format files. Facilities currently available include flexible file input.
Author: Martin Morgan, Herv\'e Pag\`es
Maintainer: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>
Citation (from within R,
enter citation("Rsamtools")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("Rsamtools")
| Rsamtools-Overview.pdf | ||
| Rsamtools-UsingCLibraries.pdf | ||
| Reference Manual |
Details
| biocViews | DataImport, HighThroughputSequencing, Sequencing, Software |
| Version | 1.4.3 |
| In Bioconductor since | BioC 2.6 (R-2.11) (6 years) |
| License | Artistic-2.0 + file LICENSE |
| Depends | methods, IRanges(>= 1.9.4), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0) |
| Imports | methods, utils, IRanges, GenomicRanges, Biostrings |
| LinkingTo | Biostrings, IRanges |
| Suggests | ShortRead, GenomicFeatures, RUnit, KEGG.db |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/release/bioc/html/Rsamtools.html |
| Depends On Me | ArrayExpressHTS, girafe, ind1KG, leeBamViews, qrqc, rnaSeqMap, ShortRead |
| Imports Me | ArrayExpressHTS, R453Plus1Toolbox, ShortRead |
| Suggests Me | GenomicRanges, R453Plus1Toolbox |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Rsamtools_1.4.3.tar.gz |
| Windows Binary | Rsamtools_1.4.3.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/Rsamtools/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/Rsamtools/ |
| Package Downloads Report | Download Stats |
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