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dPeak specifications

Information


Unique identifier OMICS_00437
Name dPeak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0.1
Stability Stable
Requirements
Perl, methods, graphics, Rcpp
Maintained Yes

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Maintainers


  • person_outline Sündüz Keleş <>
  • person_outline Dongjun Chung <>

Additional information


http://dongjunchung.github.io/dpeak/

Publication for dPeak

dPeak in pipeline

2015
PMCID: 4676285
PMID: 26670385
DOI: 10.1128/mBio.01947-15

[…] were visualized with mochiview (). the final peak list is given in  in the supplemental material. fur binding site motifs were constructed by analyzing the 100 bp upstream and downstream of the dpeak-identified peak summits, submitting the sequences to meme-chip (), and using the overrepresented sequences to construct the position weight matrix (pwm)., for chip-chip experiments, dna […]


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dPeak in publications

 (22)
PMCID: 5587812
PMID: 28911122
DOI: 10.1093/nar/gkx594

[…] fragment length of 150 bp toward the 3′ direction. to evaluate the strand imbalance, we identified a set of high signal peaks for chip-exo and se chip-seq. the subset of these peaks for which dpeak () analysis identified one or more binding events were used in fsr assessments (figure and )., we used the chip-seq qc metric definitions established by the encode consortium (,), […]

PMCID: 5452352
PMID: 28566089
DOI: 10.1186/s13059-017-1235-x

[…] with very large counts were removed to avoid bias in the pearson correlation (additional file : figure s7). to identify h3k36me3 modified nucleosome positions, we used danpos2 []. we used the “dpeak” function in danpos2 with default parameters, except for the parameter – l (read extension length) that was set to 150 bp, the size of mononucleosomal dna. genomic regions were associated […]

PMCID: 5400504
PMID: 28287392
DOI: 10.7554/eLife.22631.041

[…] individual replicate, and merged to create a representative genome track using danpos2 () which was visualised using the ucsc genome browser. peakcalling analyses were performed using the danpos2 dpeak function on untreated and treated samples in biological triplicate with matched input. merged atac-seq datasets were used to extract signal corresponding to nucleosome occupancy information […]

PMCID: 5257034
PMID: 28138368
DOI: 10.1016/j.csbj.2016.12.004

[…] freezing a liquid solution. a peak in the scattering profile represents an increase in the number of correlations at a particular qpeak, where the average separation distance between molecules is dpeak = 2π/qpeak. at q ∼ 0.09  å −1, the peak is observed for a 100  mg/ml solution, which represents an intermolecular separation distance of 70  å. as the temperature is decreased from room […]

PMCID: 5095887
PMID: 27811989
DOI: 10.1038/srep36240

[…] further denoted by subscript “avg,” which indicates the average of the variable within the high-growth period from di to dd, or “peak,” which means the spectral observation interpolated to the date dpeak when the evi was maximum. for example, vi64avg is the average normalized difference index of modis bands 6 and 4 between di and dd. the total number of variables for full-season mapping was 27 […]


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dPeak institution(s)
Department of Statistics, University of Wisconsin, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA; Department of Biochemistry, University of Wisconsin, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA; Department of Bacteriology, University of Wisconsin, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
dPeak funding source(s)
Supported by National Institutes of Health Grants(HG006716, HG007019, HG003747)), (GM045844), and (GM38660), the National Science Foundation (MCB0640642), the US Department of Energy Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-FC02- 07ER64494), the US Department of Energy BACTER Program (DE-FG02-04ER25627), and the University of Wisconsin-Madison National Institutes of Health Biotechnology Training Grant (5T32GM08349).

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