PeaKDEck specifications

Information


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

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Publication for PeaKDEck

PeaKDEck in publications

 (2)
PMCID: 4612095
PMID: 26438359
DOI: 10.1084/jem.20151323

[…] in the figure legend., atac sequencing was performed as described earlier (). the resulting library was sequenced in hiseq2000. reads were aligned with bowtie on mm9. peaks were called with peakdeck (). htseq was used to measure count density at peak sites (). areas with differential accessibility were identified with deseq2 (). go term biological enrichment was obtained by entering […]

PMCID: 4383549
PMID: 25835000
DOI: 10.1371/journal.pgen.1005061

[…] encode blacklisted regions were removed from subsequent analysis. to confirm reproducibility of faire data, peaks were called on individual faire samples using fseq v1.84 (default parameters) and peakdeck [,]. faire peaks between replicates were intersected and shown to exceed encode faire-seq guideline standards (encode and modencode guidelines for experiments generating chip, dnase, faire, […]


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PeaKDEck institution(s)
Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
PeaKDEck 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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