scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data.

Bioinformatics

Department of Statistics, University of California Riverside, Riverside, CA 92521, United States.

Published: October 2023

Summary: Here, we presented the scHiCDiff software tool that provides both nonparametric tests and parametirc models to detect differential chromatin interactions (DCIs) from single-cell Hi-C data. We thoroughly evaluated the scHiCDiff methods on both simulated and real data. Our results demonstrated that scHiCDiff, especially the zero-inflated negative binomial model option, can effectively detect reliable and consistent single-cell DCIs between two conditions, thereby facilitating the study of cell type-specific variations of chromatin structures at the single-cell level.

Availability And Implementation: scHiCDiff is implemented in R and freely available at GitHub (https://github.com/wmalab/scHiCDiff).

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10598576PMC
http://dx.doi.org/10.1093/bioinformatics/btad625DOI Listing

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