DNaseR

Application data
Created by	Pedro Madrigal
Biological application domain(s)	DNase-seq
Principal bioinformatics method(s)	DNase I footprinting
Technology	Illumina HiSeq, 454, ABI SOLiD, Ion Torrent, Illumina Solexa, Illumina
Created at	Wellcome Trust Sanger Institute
Maintained?	Yes
Input format(s)	BAM
Output format(s)	GRanges, R data.frame
Software features	stand-along software tool, can run on major computer platforms
Programming language(s)	R
Licence	GPL-2 + file LICENSE
Operating system(s)	Linux, Mac OS X, Windows

Summary: DNase I footprinting analysis of DNase-seq data.

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Description

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).