HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
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- Yih-Chii Hwang
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Chiao-Feng Lin
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Otto Valladares
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- John Malamon
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Pavel P. Kuksa
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Qi Zheng
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Brian D. Gregory
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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- Li-San Wang
- 1 Genomics and Computational Biology Graduate Program, University of Pennsylvania, 2Institute for Biomedical Informatics, University of Pennsylvania, 3Department of Pathology and Laboratory Medicine, University of Pennsylvania and 4Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
書誌事項
- 公開日
- 2014-12-04
- DOI
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- 10.1093/bioinformatics/btu801
- 公開者
- Oxford University Press (OUP)
この論文をさがす
説明
<jats:title>Abstract</jats:title> <jats:p>Summary: We implemented a high-throughput identification pipeline for promoter interacting enhancer element 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.</jats:p> <jats:p>Availability and implementation: This software package is designed to run on high-performance computing clusters with Oracle Grid Engine. 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.</jats:p> <jats:p>Contact: lswang@mail.med.upenn.edu or bdgregor@sas.upenn.edu</jats:p> <jats:p>Supplementary information: Supplementary Material is available at Bioinformatics online.</jats:p>
収録刊行物
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- Bioinformatics
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Bioinformatics 31 (8), 1290-1292, 2014-12-04
Oxford University Press (OUP)