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bioRxiv · 10.1101/2020.10.11.335273

HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

Sahin, M.·Wong, W.·Zhan, Y.·Van Deynze, K.·Koche, R.·Leslie, C. S.
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Abstract

We present HiC-DC+, a software tool for Hi-C/Hi-ChIP interaction calling and differential analysis using an efficient implementation of the HiC-DC statistical framework. HiC-DC+ integrates with popular preprocessing and visualization tools, includes TAD and A/B compartment callers, and outperformed existing tools in H3K27ac HiChIP benchmarking as validated by CRISPRi-FlowFISH. Differential HiC-DC+ analysis recovered global principles of 3D organization during cohesin perturbation and differentiation, including TAD aggregation, enhancer hubs, and promoter-enhancer loop dynamics.

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Sahin, M., Wong, W., Zhan, Y., Van Deynze, K., Koche, R., Leslie, C. S.. 2020-10-11. HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. https://doi.org/10.1101/2020.10.11.335273

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