Pavel P. Kuksa's Publications

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HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements

Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel Kuksa, Qi Zheng, Brian D. Gregory, and Li-San Wang. HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements. Bioinformatics, 2014.

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Abstract

Summary: We implemented HIPPIE (High-throughput Identification Pipeline for Promoter Interacting Enhancer elements) to streamline the workflow from mapping raw Hi-C reads, identifying DNA--DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer--target gene relationships. Availability: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine (OGE). The source code is freely available under the MIT license for academic and nonprofit use. The source code and instructions are available at the Wang lab website (http://wanglab.pcbi.upenn.edu/hippie/). It is also provided as an Amazon Machine Image to be used directly on Amazon Cloud with minimal installation.Contact: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu

BibTeX

@article{bioinf2014hippie,
	Abstract = {Summary: We implemented HIPPIE (High-throughput Identification Pipeline for Promoter Interacting Enhancer elements) to streamline the workflow from mapping raw Hi-C reads, identifying DNA--DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer--target gene relationships. Availability: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine (OGE). The source code is freely available under the MIT license for academic and nonprofit use. The source code and instructions are available at the Wang lab website (http://wanglab.pcbi.upenn.edu/hippie/). It is also provided as an Amazon Machine Image to be used directly on Amazon Cloud with minimal installation.Contact: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu},
	Author = {Hwang, Yih-Chii and Lin, Chiao-Feng and Valladares, Otto and Malamon, John and Kuksa, Pavel and Zheng, Qi and Gregory, Brian D. and Wang, Li-San},
	Bib2Html_Pubtype = {Journal},
	Date-Added = {2014-12-05 20:47:26 +0000},
	Date-Modified = {2020-03-06 13:18:40 -0500},
	Doi = {10.1093/bioinformatics/btu801},
	Eprint = {http://bioinformatics.oxfordjournals.org/content/early/2014/12/04/bioinformatics.btu801.full.pdf+html},
	Journal = {Bioinformatics},
	Title = {{HIPPIE}: A high-throughput identification pipeline for promoter interacting enhancer elements},
	Url = {http://bioinformatics.oxfordjournals.org/content/early/2014/12/04/bioinformatics.btu801.abstract},
	Year = {2014},
	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/content/early/2014/12/04/bioinformatics.btu801.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/bioinformatics/btu801}}

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