HIPPIE: A High-Throughput Identification Pipeline for Promoter Interacting Enhancer elements



HIPPIE is the workflow for analyzing batches of Hi-C paired-end reads in compressed FASTQ format (.fastq.gz) 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.



*The test fastq.gz files consist mainly chromosome1 and chromosome2 reads from an original Hi-C experiment (Lieberman-Aiden et al. Science 2009) GEO accession: GSM455139 and GSM455140.



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. (2014, Bioinformatics) [DOI:10.1093/bioinformatics/btu801]


Release Notes

[2015/04/26] Release of HIPPIE v0.0.2-beta. Major changes:

There are also some minor fixing to improve the pipeline efficiency.

[2015/03/16] First release of HIPPIE v0.0.1-beta.

[2014/05/08] Website created and source code released.


HIPPIE is released under the MIT license and is available for academic and nonprofit use for free.


[Last update: 2015/4/26]

Questions? yihhwang [at] mail.med.upenn.edu | Wang Lab | The Institute for Biomedical Informatics | University of Pennsylvania