A peak-calling algorithm written in Perl, mainly intended for use in the identification of peaks in mapped DNaseI-seq data. PeaKDEck also includes a set of utilities for processing and manipulation of this data. It selects a threshold read density for peak calling by constructing a probability distribution of background read density scores using kernel density estimation. PeaKDEck can be used for similar methods such as chromatin immunoprecipitation sequencing and FAIRE-seq, by applying a user-defined offset to calculated genomic positions. It is especially useful compared with other peak callers where signal-to-noise ratio is low.