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

DNaseR

DNase I footprinting analysis of DNase-seq data

Bioconductor version: 2.13

Strand-specific digital genomic footprinting in DNase-seq data. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific bias).

Author: Pedro Madrigal <pm at engineering.com>

Maintainer: Pedro Madrigal <pm at engineering.com>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DNaseR")

 

PDF	R Script	DNaseR Vignette
PDF		Reference Manual
Text		LICENSE

Details

biocViews	Genetics, Software, Transcription
Version	1.0.0
In Bioconductor since	BioC 2.13 (R-3.0)
License	GPL-2 + file LICENSE
Depends	R (>= 2.10.0), IRanges
Imports	Rsamtools, GenomicRanges
Suggests	RUnit, BiocGenerics
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source	DNaseR_1.0.0.tar.gz
Windows Binary	DNaseR_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	DNaseR_1.0.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats