HIPPIE

The software tool 'HIPPIE' is a high-throughput identification pipeline for identifying enhancer elements that interact with promoters. It streamlines the workflow from mapping raw Hi-C reads, identifying interacting fragments, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible enhancer-target gene relationships. The package is designed to run on high-performance computing clusters.

Topic

Molecular interactions, pathways and networks;Mapping;Epigenetics;Transcription factors and regulatory sites

Detail

  • Operation: Pathway or network prediction;DNA mapping

  • Software interface: Command-line user interface

  • Language: R;Perl;Python

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Institute on Agingand National Institute of General Medical Sciences.

  • Input: -

  • Output: -

  • Contact: mkmoon@mail.med.upenn.edu

  • Collection: -

  • Maturity: -

Publications

  • HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements.
  • Hwang YC, et al. HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. 2015; 31:1290-2. doi: 10.1093/bioinformatics/btu801
  • https://doi.org/10.1093/bioinformatics/btu801
  • PMID: 25480377
  • PMC: PMC4393516

Download and documentation

    Currently not available or not maintained.

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