DNaseR
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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) | Nucleic acid sequence feature detection, Peak calling |
| 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 is an R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. It relies on the Skellam distribution (correlation of two Poisson distributions) to detect narrow-depleted regions of read-enrichment formed by the mapped reads in the forward and reversed DNA strands. Its main characteristic consists in that consensus DNA sequences (motifs) search is not required a priori to detect footprints.
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References
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