To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

Rsamtools

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

Bioconductor version: Release (3.0)

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Author: Martin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel Hayden

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

Citation (from within R, enter citation("Rsamtools")):

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
Video   pileup in Rsamtools

Details

biocViews Alignment, Coverage, DataImport, QualityControl, Sequencing, Software
Version 1.18.2
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0 | file LICENSE
Depends methods, S4Vectors(>= 0.1.0), IRanges(>= 1.99.17), GenomeInfoDb(>= 1.1.3), GenomicRanges(>= 1.17.19), XVector(>= 0.5.3), Biostrings(>= 2.33.11)
Imports utils, BiocGenerics(>= 0.1.3), zlibbioc, bitops
Suggests GenomicAlignments, 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, chimera, CoverageView, deepSNV, ESNSTCC, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, ggtut, girafe, leeBamViews, methylPipe, MMDiff, oneChannelGUI, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, ssviz, systemPipeR, TBX20BamSubset, TEQC, TitanCNA, VariantAnnotation, wavClusteR
Imports Me AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, BSgenome, CAGEr, casper, CexoR, ChIPQC, cn.mops, CNVrd2, compEpiTools, csaw, customProDB, deepSNV, derfinder, DEXSeq, DNaseR, DOQTL, easyRNASeq, EDASeq, epigenomix, exonfindR, FourCSeq, FunciSNP, GenomicAlignments, GenomicInteractions, ggbio, GGtools, gmapR, Gviz, gwascat, h5vc, HTSeqGenie, LungCancerLines, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MEDIPS, PICS, QDNAseq, QuasR, R453Plus1Toolbox, Rariant, Repitools, rtracklayer, SGSeq, tracktables, trackViewer, TransView, VariantFiltering, VariantTools
Suggests Me AnnotationHub, BaseSpaceR, BiocParallel, biomvRCNS, DiffBind, gage, GenomeInfoDb, GenomicFeatures, GenomicRanges, ind1KG, metaseqR, parathyroidSE, QuasR, RnaSeqTutorial, seqbias, SigFuge, SplicingGraphs, Streamer

Package Archives

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

Package Source Rsamtools_1.18.2.tar.gz
Windows Binary Rsamtools_1.18.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Rsamtools_1.18.2.tgz
Mac OS X 10.9 (Mavericks) Rsamtools_1.18.2.tgz
Browse/checkout source (username/password: readonly)
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