Nature CommunicationsBioinformaticsPeer-reviewed journal article
HiC-DC+: systematic 3D interaction calls and differential analysis for Hi-C and HiChIP
Merve ŞahiniD, Wilfred WongiD, Yingqian Ada ZhaniD, Kinsey Van DeynzeiD, Richard P. KocheiD, Christina S. LeslieiD
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.
- assay: Hi-C
- research focus: differential expression
- research focus: gene regulatory network inference
- approach: statistical model
- Citations
- 61
- FWCI
- 3.14
- Field percentile
- top 6%
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