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CSDeconv specifications


Unique identifier OMICS_00436
Name CSDeconv
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 1.0.3
Stability Stable
Optimization Toolbox, Statistics Toolbox
Maintained Yes




No version available


  • person_outline Desmond Lun

Publication for CSDeconv

CSDeconv citations


The ECF sigma factor, PSPTO_1043, in Pseudomonas syringae pv. tomato DC3000 is induced by oxidative stress and regulates genes involved in oxidative stress response

PLoS One
PMCID: 5507510
PMID: 28700608
DOI: 10.1371/journal.pone.0180340

[…] the method described in []. version 2.20 of the soap2 alignment package [] was used. regions enriched by immunoprecipitation, here referred to as peaks, were identified computationally using csdeconv [] version 1.02, as described in [] (with parameters llr = 3 and alpha = 1000). several peaks fell within the pspto_1043 gene. since these were probably artifacts due to dna recovered […]


The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally

PLoS Genet
PMCID: 3798270
PMID: 24146625
DOI: 10.1371/journal.pgen.1003839

[…] was good agreement between the chip-chip and chip-seq datasets (109 peaks in common). however, 15 regions identified by chip-chip were resolved into 32 binding regions () using chip-seq and the csdeconv peak deconvolution algorithm . for example, compared to only one binding region resolved with chip-chip, three binding regions were identified upstream of cyda () and two were identified […]


Evaluation of Algorithm Performance in ChIP Seq Peak Detection

PLoS One
PMCID: 2900203
PMID: 20628599
DOI: 10.1371/journal.pone.0011471

[…] “directional scoring methods,” are more appropriate for proteins that bind to specific sites (transcription factors), rather than more distributed binders, such as histones or rna polymerase ()., csdeconv, a recently published algorithm, uses both g-kde and directional information in conjunction with a deconvolution approach, which enables detection of closely spaced binding sites . […]

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CSDeconv institution(s)
Phenomics and Bioinformatics Research Centre, School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA, Australia; Australian Centre for Plant Functional Genomics, University of South Australia, Mawson Lakes, SA, Australia; Seattle Biomedical Research Institute, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Biomedical Engineering and Department of Microbiology, Boston University, Boston, MA, USA

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