Rsamtools

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

Bioconductor version: 2.10

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
Depends methods, IRanges(>= 1.13.30), GenomicRanges(>= 1.7.43), Biostrings(>= 2.21.12)
Imports methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc, bitops, BiocGenerics(>= 0.1.3)
Suggests ShortRead(>= 1.13.19), GenomicFeatures, RUnit, KEGG.db
System Requirements
License Artistic-2.0 + file LICENSE
URL http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me ArrayExpressHTS, BitSeq, deepSNV, easyRNASeq, EDASeq, exomeCopy, GGtools, girafe, ind1KG, leeBamViews, oneChannelGUI, qrqc, ReQON, rnaSeqMap, ShortRead, TEQC, VariantAnnotation
Imports Me ArrayExpressHTS, biovizBase, deepSNV, ggbio, R453Plus1Toolbox, rtracklayer, ShortRead, VariantAnnotation
Suggests Me GenomicRanges, R453Plus1Toolbox, RnaSeqTutorial, seqbias, Streamer
Version 1.8.6
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source Rsamtools_1.8.6.tar.gz
Windows Binary Rsamtools_1.8.6.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Rsamtools_1.8.6.tgz
Package Downloads Report Download Stats

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