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PeaKDEck | A kernel density estimator-based peak calling program for DNaseI-seq data

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.

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PeaKDEck classification

PeaKDEck specifications

Unique identifier:
OMICS_02207
Interface:
Command line interface, Graphical user interface
Input data:
DNaseI-seq
Output data:
Numerical sorting, Sam filter, Random read selection, Density analysis, Peak calling, Size ordering of peaks
Programming languages:
Perl
Version:
1.1
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Input format:
SAM
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable

PeaKDEck distribution

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PeaKDEck classification

PeaKDEck specifications

Unique identifier:
OMICS_02207
Interface:
Graphical user interface
Input data:
DNaseI-seq
Output data:
Numerical sorting, Sam filter, Random read selection, Density analysis, Peak calling, Size ordering of peaks
Programming languages:
Perl, Other
Version:
1.1
Software type:
Restrictions to use:
None
Input format:
SAM
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Medium
Stability:
Stable

PeaKDEck distribution

versioning

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PeaKDEck support

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Publications

Institution(s)

Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

Funding source(s)

Medical Research Council grants (MRC G0901998, MRC G116/165) and National Institute for Health Research Oxford Comprehensive Biomedical Research Centre (BRC) Program

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