Difference between revisions of "DNaseR"
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Revision as of 12:50, 26 October 2013
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Application data |
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| Created by | Pedro Madrigal |
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| 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 | R/Bioconductor package, can run on major computer platforms |
| Programming language(s) | R |
| Licence | GPL-2 + file LICENSE |
| Operating system(s) | Linux, Mac OS X, Windows |
| Contact: | pm@engineering.com |
Summary: DNase I footprinting analysis of DNase-seq data in R
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Description
DNaseR performs trand-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).
Links
References
To add a reference for DNaseR, enter the PubMed ID in the field below and click 'Add'.
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