DBChIP protocols

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DBChIP specifications

Information


Unique identifier OMICS_00470
Name DBChIP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 1.1.6
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Kun Liang <>

Publication for DBChIP

DBChIP in pipeline

2013
PMCID: 3717085
PMID: 23721376
DOI: 10.1186/1471-2105-14-169

[…] sidestep the issue of different ip efficiencies by focussing on regions with high signal to background ratio and normalizing the counts on these regions only. finally, one of the latest methods, dbchip [], allows the inclusion of biological replicates in the model, but does not account for their different ip efficiencies in the detection of enriched and differentially bound regions., […]


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DBChIP in publications

 (9)
PMCID: 5142015
PMID: 26764273
DOI: 10.1093/bib/bbv110

[…] hence, the choice of p-value threshold is crucial for the first class of tools, as this number can vary abruptly by several orders of magnitude. as for the tools with a small number of dr (mmdiff, dbchip), this number indeed increases when relaxing the threshold, but remains at a low level, much lower than other tools from the same class, indicating an intrinsic difference in the internal […]

PMCID: 4676285
PMID: 26670385
DOI: 10.1128/mBio.01947-15

[…] data sets were normalized to 20 million reads, and 262 peaks of low read count (<2,500 reads at the peak summit) were removed because they were present in both fur+ and iron-deficient cultures (dbchip []; p < 0.05) or did not visually conform to a peak above the local background. normalized chip-seq data files were visualized with mochiview (). the final peak list is given in  in […]

PMCID: 4310510
PMID: 25657574
DOI: 10.4137/CIN.S13972

[…] peak locations., several parametric methods based on poisson/negative binomial distribution have been proposed to address this differential enrichment problem in chip-seq data such as diffbind and dbchip., most of these methods require biological replications to estimate the parameters, especially the dispersion parameter in the negative binomial model. however, many chip-seq data usually […]

PMCID: 4257862
PMID: 25401693
DOI: 10.1038/nm.3716

[…] a t-test to verify the null hypothesis that the cy3/cy5 intensity log ratios derived from gskj4-treated cells (24 and 72 h; two replicates per time point) are distinct from 0. the r package dbchip was used to identify sequences for which differential k27me3-immunoprecipitated is associated with gskj4 treatment. enrichment sites estimated from vehicle-treated sf8628 cells and sf8628 […]

PMCID: 4224375
PMID: 25380244
DOI: 10.1371/journal.pone.0109691

[…] consistent results across the large numbers of datasets we have considered. although we considered more formal testing approaches (e.g., differential enrichment analysis of the input samples with dbchip and irreducible discovery rate (idr) ) for comparing two or more input samples, the overall insufficient depths of the input samples (median depths ranged between 0 to 28 for the c. elegans […]


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DBChIP institution(s)
Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
DBChIP funding source(s)
National Institutes of Health grant HG003747, Department of Energy grant FG02-04ER25627

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