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")
PDF An introduction to Rsamtools
PDF Using samtools C libraries
PDF 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

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