scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data

Abstract

SummaryQuantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) data and to integrate it with other single-cell data modalities. We present single-cell gene associating domain (scGAD) scores as a dimension reduction and exploratory analysis tool for scHi-C data. scGAD enables summarization at the gene level while accounting for inherent gene-level genomic biases. Low-dimensional projections with scGAD capture clustering of cells based on their 3D structures. scGAD enables identifying genes with significant chromatin interactions within and between cell types. We further show that scGAD facilitates the integration of scHi-C data with other single-cell data modalities by enabling its projection onto reference low-dimensional embeddings. AvailabilityscGAD is part of the BandNorm R package at https://sshen82.github.io/BandNorm/articles/scGAD-tutorial.html. Contactkeles@stat.wisc.edu, yzheng23@fredhutch.org Supplementary informationSupplementary data are available at Bioinformatics online.