To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

DNaseR

DNase I footprinting analysis of DNase-seq data

Bioconductor version: Release (2.14)

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 <pm12 at sanger.ac.uk>

Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>

Citation (from within R, enter citation("DNaseR")):

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 1.2.0
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_1.2.0.tar.gz
Windows Binary DNaseR_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DNaseR_1.2.0.tgz
Mac OS X 10.9 (Mavericks) DNaseR_1.2.0.tgz
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