DNase I footprinting analysis of DNase-seq data

Bioconductor version: Development (3.0)

Strand-specific digital genomic footprinting in 'double-hit' 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 biases).

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

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

To install this package, start R and enter:


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


PDF R Script DNaseR Vignette
PDF   Reference Manual


biocViews Genetics, Software, Transcription
Version 1.3.3
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-2 + file LICENSE
Depends R (>= 2.10.0), BiocGenerics, S4Vectors, IRanges
Imports GenomeInfoDb, GenomicRanges, Rsamtools
Suggests RUnit, BiocGenerics
System Requirements
Depends On Me
Imports Me
Suggests Me

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Package Source DNaseR_1.3.3.tar.gz
Windows Binary DNaseR_1.3.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) DNaseR_1.3.3.tgz
Mac OS X 10.9 (Mavericks) DNaseR_1.3.3.tgz
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