Rsamtools

Import aligned BAM file format sequences into R / Bioconductor

Bioconductor version: 2.8

This package provides an interface to the 'samtools' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map) format files. Facilities currently available include flexible file input.

Author: Martin Morgan, Herv\'e Pag\`es

Maintainer: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

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

Details

biocViews DataImport, Sequencing, HighThroughputSequencing
Depends methods, IRanges(>= 1.9.4), GenomicRanges(>= 0.1.0), Biostrings(>= 2.15.0)
Imports methods, utils, IRanges, GenomicRanges, Biostrings
Suggests ShortRead, 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, girafe, ind1KG, leeBamViews, qrqc, rnaSeqMap, ShortRead
Imports Me ArrayExpressHTS, R453Plus1Toolbox, ShortRead
Suggests Me GenomicRanges, R453Plus1Toolbox
Version 1.4.3
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source Rsamtools_1.4.3.tar.gz
Windows Binary Rsamtools_1.4.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Rsamtools_1.4.3.tgz
Package Downloads Report Download Stats

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