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 2.12 of Bioconductor; for the stable, up-to-date release version, see Rsamtools.

Binary alignment (BAM), variant call (BCF), or tabix file import

Bioconductor version: 2.12

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	R Script	An introduction to Rsamtools
PDF	R Script	Using samtools C libraries
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, HighThroughputSequencing, Sequencing, Software
Version	1.12.4
In Bioconductor since	BioC 2.6 (R-2.11) (6 years)
License	Artistic-2.0 + file LICENSE
Depends	methods, IRanges(>= 1.15.35), GenomicRanges(>= 1.11.38), Biostrings(>= 2.25.6)
Imports	methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics(>= 0.1.3)
LinkingTo	Biostrings, IRanges
Suggests	ShortRead(>= 1.13.19), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset, RUnit, TxDb.Hsapiens.UCSC.hg18.knownGene
SystemRequirements
Enhances
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BitSeq, casper, chimera, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, ggtut, girafe, leeBamViews, MMDiff, oneChannelGUI, prebs, qrqc, r3Cseq, Rcade, ReQON, RIPSeeker, RNASeqDataSubset, rnaSeqMap, ShortRead, TBX20BamSubset, TEQC, VariantAnnotation
Imports Me	annmap, ArrayExpressHTS, biovizBase, CAGEr, cn.mops, deepSNV, DEXSeq, FunciSNP, ggbio, gmapR, Gviz, HTSeqGenie, LungCancerLines, MEDIPS, PICS, QuasR, R453Plus1Toolbox, rtracklayer, ShortRead, TransView, VariantAnnotation, VariantTools
Suggests Me	AnnotationHub, biomvRCNS, DiffBind, GenomicFeatures, GenomicRanges, ind1KG, parathyroidSE, QuasR, R453Plus1Toolbox, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, seqbias, SplicingGraphs, Streamer
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	Rsamtools_1.12.4.tar.gz
Windows Binary	Rsamtools_1.12.4.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Rsamtools_1.12.4.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/Rsamtools/tree/release-2.12
Package Short Url	http://bioconductor.org/packages/Rsamtools/
Package Downloads Report	Download Stats

Documentation »

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