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map3C: a computational tool for processing multiomic single-cell Hi-C data.

Joseph Galasso·Ye Wang·Frank Alber·Jason Ernst·Chongyuan Luo
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Abstract

SUMMARY: The emergence of multiomic single-cell Hi-C (scHi-C) methods, which simultaneously profile chromatin conformation and other modalities such as gene expression or DNA methylation, creates tremendous opportunities for studying the genome's structure-function relationships. Existing tools for processing multiomic scHi-C datasets lack certain key functions for downstream bioinformatics analysis. We present map3C, a software tool that incorporates additional key functions. Specifically, we demonstrate that map3C facilitates multiomic scHi-C processing, quality control, and identification of structural variant locations in the genome. AVAILABILITY AND IMPLEMENTATION: map3C is available at https://github.com/luogenomics/map3C and is archived at https://doi.org/10.5281/zenodo.20724719.

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SoftwareMultiomicsSingle-Cell AnalysisComputational BiologyChromatinGenomicsHumansJournal ArticleResearch Support, N.I.H., Extramural

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Joseph Galasso, Ye Wang, Frank Alber, Jason Ernst, Chongyuan Luo. 2026-08-03. map3C: a computational tool for processing multiomic single-cell Hi-C data.. https://doi.org/10.1093/bioinformatics%2Fbtag562

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