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Protocols

CSDeconv specifications

Information


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
Requirements
Optimization Toolbox, Statistics Toolbox
Maintained Yes

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Versioning


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Maintainer


  • person_outline Desmond Lun

Publication for CSDeconv

CSDeconv citations

 (4)
library_books

Ritornello: high fidelity control free chromatin immunoprecipitation peak calling

2017
Nucleic Acids Res
PMCID: 5716106
PMID: 28981893
DOI: 10.1093/nar/gkx799

[…] nal and noise.Binding events can also occur in close proximity to one another and it is often difficult to resolve how many binding sites are present and precisely where binding occurs. BRACIL () and CSDeconv () use blind deconvolution algorithms to resolve individual peaks at multi-binding loci but are not scalable for peak calling and are thus used for post processing when peaks have been identi […]

call_split

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

2017
PLoS One
PMCID: 5507510
PMID: 28700608
DOI: 10.1371/journal.pone.0180340
call_split See protocol

[…] ollowing 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 from th […]

call_split

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

2013
PLoS Genet
PMCID: 3798270
PMID: 24146625
DOI: 10.1371/journal.pgen.1003839
call_split See protocol

[…] ter than 90% and 80% of these reads, respectively, mapped uniquely to the K12 MG1655 genome (version U00096.2) using the software package SOAP release 2.20, allowing no more than two mismatches . The CSDeconv algorithm was then used to determine significantly enriched regions in high resolution using both ChIP-seq replicates and two anaerobic input samples from the same sequencing run as the Arc […]

library_books

Evaluation of Algorithm Performance in ChIP Seq Peak Detection

2010
PLoS One
PMCID: 2900203
PMID: 20628599
DOI: 10.1371/journal.pone.0011471

[…] call “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 . Such an ap […]

Citations

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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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