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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("DNaseR")

Documentation

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 Downloads

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)
Package Downloads Report Download Stats

Mailing Lists »

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

Fred Hutchinson Cancer Research Center