Rsamtools

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

Bioconductor version: Release (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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("Rsamtools")

Documentation

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)
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)
Suggests	ShortRead(>= 1.13.19), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset, RUnit, TxDb.Hsapiens.UCSC.hg18.knownGene
System Requirements
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	ArrayExpressHTS, BitSeq, casper, chimera, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, 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, 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

Package Downloads

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
Package Downloads Report	Download Stats