HIPPIE is the workflow for analyzing 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.
Wang Lab @ IBI
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HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements.
Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa P, Zheng Q, Gregory BD, Wang LS.
Bioinformatics. 2014 Dec 4. pii: btu801.