scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37847655.
- Also identified by DOI 10.1093/bioinformatics/btad625 and PMC identifier 10598576.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. scHiCDiff is implemented in R and freely available at GitHub (https://github.com/wmalab/scHiCDiff).
Medical subject headings
- Chromatin
- Carcinoma, Intraductal, Noninfiltrating