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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 2.10 of Bioconductor; for the stable, up-to-date release version, see Rsamtools.
Binary alignment (BAM), variant call (BCF), or tabix file import
Bioconductor version: 2.10
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Author: Martin Morgan, Herv\'e Pag\`es
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
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")
| An introduction to Rsamtools | ||
| Using samtools C libraries | ||
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | DataImport, HighThroughputSequencing, Sequencing, Software |
| Version | 1.8.6 |
| In Bioconductor since | BioC 2.6 (R-2.11) (6 years) |
| License | Artistic-2.0 + file LICENSE |
| Depends | methods, IRanges(>= 1.13.30), GenomicRanges(>= 1.7.43), Biostrings(>= 2.21.12) |
| Imports | methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics(>= 0.1.3) |
| LinkingTo | Biostrings, IRanges |
| Suggests | ShortRead(>= 1.13.19), GenomicFeatures, RUnit, KEGG.db |
| SystemRequirements | |
| Enhances | |
| URL | http://bioconductor.org/packages/release/bioc/html/Rsamtools.html |
| Depends On Me | ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, ggtut, girafe, ind1KG, leeBamViews, oneChannelGUI, qrqc, ReQON, rnaSeqMap, ShortRead, TEQC, VariantAnnotation |
| Imports Me | ArrayExpressHTS, biovizBase, cn.mops, deepSNV, ggbio, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation |
| Suggests Me | GenomicRanges, R453Plus1Toolbox, RnaSeqTutorial, seqbias, Streamer |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | Rsamtools_1.8.6.tar.gz |
| Windows Binary | Rsamtools_1.8.6.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/Rsamtools/tree/release-2.10 |
| Package Short Url | http://bioconductor.org/packages/Rsamtools/ |
| Package Downloads Report | Download Stats |
Documentation »
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