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HIPPIE is the workflow for analyzing batches of Hi-C paired-end reads in FASTQ format and predict enhancer–target gene interactions. HIPPIE streamlines the entire processing phase including reads mapping, quality control and enhancer–target gene prediction as well as characterizing the interactions.
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Check our [website] (http://wanglab.pcbi.upenn.edu/hippie/) for instruction of installation and usage.
If you use HIPPIE for your research, please use the following citation:
Hwang Y-C, Lin C-F, Valladares O, Malamon J, Kuksa P P, Zheng Q, Gregory B D, and Wang L-S. HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements. (2015, Bioinformatics) [DOI] (http://doi.org/10.1093/bioinformatics/btu801)