PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data.
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ABSTRACT:
SUBMITTER: McCarthy MT
PROVIDER: S-EPMC3998130 | biostudies-literature | 2014 May
REPOSITORIES: biostudies-literature
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PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data.
McCarthy Michael T MT O'Callaghan Christopher A CA
Bioinformatics (Oxford, England) 20140108 9
Hypersensitivity to DNaseI digestion is a hallmark of open chromatin, and DNaseI-seq allows the genome-wide identification of regions of open chromatin. Interpreting these data is challenging, largely because of inherent variation in signal-to-noise ratio between datasets. We have developed PeaKDEck, a peak calling program that distinguishes signal from noise by randomly sampling read densities and using kernel density estimation to generate a dataset-specific probability distribution of random ...[more]
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