Rsamtools

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

Citation (from within R, 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, Sequencing, Software
Version 1.16.1
In Bioconductor since BioC 2.6 (R-2.11)
License Artistic-2.0 | file LICENSE
Depends methods, IRanges(>= 1.21.10), GenomicRanges(>= 1.15.11), XVector(>= 0.3.2), Biostrings(>= 2.31.3), GenomeInfoDb(>= 0.99.17)
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, CNVrd2, CoverageView, deepSNV, EDASeq, exomeCopy, exomePeak, GenomicAlignments, GenomicFiles, ggtut, girafe, leeBamViews, MMDiff, oneChannelGUI, qrqc, r3Cseq, Rcade, ReQON, rfPred, RIPSeeker, rnaSeqMap, ShortRead, TBX20BamSubset, TEQC, VariantAnnotation
Imports Me AllelicImbalance, annmap, ArrayExpressHTS, biovizBase, BSgenome, CAGEr, casper, CexoR, ChIPQC, cn.mops, customProDB, deepSNV, DEXSeq, DNaseR, easyRNASeq, FunciSNP, GenomicAlignments, 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, trackViewer, TransView, VariantFiltering, VariantTools
Suggests Me AnnotationHub, BaseSpaceR, biomvRCNS, DESeq2, DiffBind, gage, GenomicFeatures, GenomicRanges, ind1KG, metaseqR, parathyroidSE, QuasR, RnaSeqTutorial, seqbias, SigFuge, SplicingGraphs, Streamer

Package Downloads

Package Source Rsamtools_1.16.1.tar.gz
Windows Binary Rsamtools_1.16.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Rsamtools_1.16.1.tgz
Mac OS X 10.9 (Mavericks) Rsamtools_1.16.1.tgz
Package Downloads Report Download Stats

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