Rsamtools

Import aligned BAM file format sequences into R / Bioconductor

Bioconductor version: 2.7

This package provides an interface to the 'samtools' utilities 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		Reference Manual

Details

biocViews	DataImport, Sequencing, HighThroughputSequencing
Depends	methods, IRanges(>= 1.7.23), 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
URL	http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Depends On Me	girafe, ind1KG, leeBamViews, ShortRead
Imports Me	R453Plus1Toolbox, ShortRead
Suggests Me	GenomicRanges, R453Plus1Toolbox
Version	1.2.3
Since	Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source	Rsamtools_1.2.3.tar.gz
Windows Binary	Rsamtools_1.2.3.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	Rsamtools_1.2.3.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center