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EnhancerFinder specifications

Information


Unique identifier OMICS_15094
Name EnhancerFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Tony Capra <>

Publication for EnhancerFinder

EnhancerFinder in publications

 (8)
PMCID: 5657043
PMID: 29072144
DOI: 10.1186/s12859-017-1828-0

[…] hidden layers being 50-50-200. the input for the model is the matrix with enhancer samples as rows and features as columns. here, we first compared our method with five existing methods, including enhancerfinder [], clare [], deep [], chromhmm and segway in roc space. note that comparisons with the existing methods are not easy due to the fact that most existing methods were developed […]

PMCID: 5737616
PMID: 28985297
DOI: 10.1093/gbe/evx194

[…] we then trained a linear svm to distinguish the two classes of enhancers. the kernel was normalized using the square root diagonal kernel normalizer. all training and testing was done in the enhancerfinder framework ()., k-mer spectra quantify sequence content with the frequency of each unique nucleotide combination of length k in the enhancer sequence. we determined the k-mer spectra […]

PMCID: 5461523
PMID: 28589862
DOI: 10.1186/s12920-017-0264-3

[…] to the earlier results by erwin et al. (see fig. ) especially when one considers the difference in size of feature sets (besides k-mers and evolutionary conservation 2496 features were used for enhancerfinder training, comparing to 8 for our h1hesc or 78 for tier1&2 classifier). while the best performance of enhancerfinder is higher, it is only achieved when it is using evolutionary […]

PMCID: 5059478
PMID: 27703156
DOI: 10.1038/ncomms12923

[…] of all regions in the meta-analysis. this procedure was repeated separately for each of the three scores., we compared our unsupervised enhancer prediction against two previously reported methods, enhancerfinder and emerge. unless otherwise noted (), area under the curve for receiver operating characteristic curves for enhancerfinder and emerge results are those reported in the corresponding […]

PMCID: 5772166
PMID: 27095202
DOI: 10.1093/nar/gkw278

[…] data (), ideas yielded notably better predictions by its enhancer-labeled states (enh, enhf, enhw) than by other methods (). ideas also performed better in fantom5 and cage data when compared with enhancerfinder (), a supervised method that was trained on vista enhancers, suggesting an advantage of using unsupervised approaches to identify novel enhancers that are not represented […]


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EnhancerFinder institution(s)
Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Department of Developmental Biology and Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PE, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, TE, USA; Duke University, Durham, NC, USA
EnhancerFinder funding source(s)
This project was supported by NIH grants from NIGMS (GM082901, GM61390), NHGRI (HG005058, HG006768), NICHD (HD059862), NIDDK (DK090382), NINDS (NS079231), and NHLBI (HL098179). It was also funded by a PhRMA Foundation fellowship, a University of California Achievement Awards for College Scientists (ARCS) Scholarship, a gift from the San Simeon Fund (URL unavailable), and institutional funds from the Gladstone Institute as well as institutional funds from Vanderbilt University.

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