source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

Rsamtools

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

Bioconductor version: 2.13

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, Valerie Obenchain

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R and enter:

source("http://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	1.14.3
In Bioconductor since	BioC 2.6 (R-2.11)
License	Artistic-2.0 | file LICENSE
Depends	methods, IRanges(>= 1.19.11), GenomicRanges(>= 1.13.35), XVector, Biostrings(>= 2.29.7)
Imports	utils, BiocGenerics(>= 0.1.3), zlibbioc, bitops
Suggests	ShortRead(>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle
System Requirements
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BitSeq, casper, chimera, CNVrd2, deepSNV, easyRNASeq, EDASeq, exomeCopy, exomePeak, GGtools, ggtut, girafe, leeBamViews, MMDiff, oneChannelGUI, prebs, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, TBX20BamSubset, TEQC, VariantAnnotation
Imports Me	AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, CAGEr, CexoR, cn.mops, customProDB, deepSNV, DEXSeq, DNaseR, FunciSNP, ggbio, gmapR, Gviz, HTSeqGenie, LungCancerLines, MEDIPS, PICS, QuasR, R453Plus1Toolbox, Repitools, rtracklayer, TransView, VariantAnnotation, VariantTools
Suggests Me	AnnotationHub, biomvRCNS, DiffBind, gage, GenomicFeatures, GenomicRanges, ind1KG, parathyroidSE, QuasR, R453Plus1Toolbox, RNAseqData.HNRNPC.bam.chr14, RnaSeqTutorial, seqbias, SigFuge, SplicingGraphs, Streamer

Package Archives

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

Package Source	Rsamtools_1.14.3.tar.gz
Windows Binary	Rsamtools_1.14.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	Rsamtools_1.14.3.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats