DNase2TF protocols

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DNase2TF specifications

Information


Unique identifier OMICS_11373
Name DNase2TF
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
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gordon Lager <>

Publication for DNase2TF

DNase2TF in pipeline

2015
PMCID: 4514710
PMID: 26208222
DOI: 10.1371/journal.pone.0133280

[…] methods for prediction of tf binding using dgf have been described in different cell-types from yeast to human [–,–]. different computational prediction tools such as wellington [], centipede [], dnase2tf [] and footprint detection software [] are available. we have devised an approach that uses dgf datasets from [], in combination with motiflab [] and four c-myb motifs from the transfac […]


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DNase2TF in publications

 (3)
PMCID: 5893535
PMID: 29636475
DOI: 10.1038/s41467-018-03856-y

[…] identified 485 tf motifs in the retina dataset and 521 motifs in the rpe dataset. we first scanned all potential tf binding motifs (p value < 1.0−4) across the human genome using fimo. we used dnase2tf to identify all potential functional tf binding site using footprinting analysis in open regions (atac-seq peaks) in both the retina and rpe samples. we next identified tf footprints […]

PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] using various algorithms and tf-binding site tools, such as v-plots [,]. for dnase-seq, regulatory elements in open chromatin regions are identified using footprinting algorithms. among these tools, dnase2tf [] offers better detection accuracy and requires less computing time. in the analysis of atac-seq data, the positions of both nucleosome and tf-binding chromatin are identified using […]

PMCID: 4514710
PMID: 26208222
DOI: 10.1371/journal.pone.0133280

[…] methods for prediction of tf binding using dgf have been described in different cell-types from yeast to human [–,–]. different computational prediction tools such as wellington [], centipede [], dnase2tf [] and footprint detection software [] are available. we have devised an approach that uses dgf datasets from [], in combination with motiflab [] and four c-myb motifs from the transfac […]


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DNase2TF institution(s)
Laboratory of Receptor Biology and Gene Expression, NIH, Bethesda, MD, USA
DNase2TF funding source(s)
This research was supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.

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