Calling loops from HiChIP data with hichipper


hichipper is an open-source command-line toolkit that performs restriction fragment bias-aware preprocessing of HiChIP data. This package takes output from a HiC-Pro run and a sample manifest file (.yaml) that coordinates optional high-quality peaks (identified through ChIP-Seq) and restriction fragment locations as input and produces output that can be used to 1) determine library quality, 2) identify and characterize DNA loops and 3) interactively visualize loops. Loops are assigned strength and confidence metrics that can be used to evaluate samples individually or for differential analysis in downstream tools.



The primary developer is Caleb Lareau in the Aryee Lab.


If you use hichipper in your research, please cite our tool at the following URL:

Bugs / Errors

Please let us know if you find any errors/inconsistencies in the documentation or code by filing a new Github Issue.