Our review article is published in Genomics, Proteomics & Bioinformatics:

This review provides a concise end-to-end overview of published scATAC-seq workflows, spanning preprocessing to downstream analyses including quality control, alignment, peak calling, dimensionality reduction, clustering, gene regulation score calculation, cell type annotation, and multiomics integration. It also surveys key scATAC-seq databases, discusses emerging deep-learning and AI foundation-model approaches, and highlights recent advances in spatial ATAC-seq and related computational methods, with the goal of helping researchers choose appropriate tools and build customized analysis workflows.

Wang C, Zhou J, Zhang H, Zhuang Z, Bai G, Tang M, Liu S, Liu T. Computational Analyses and Challenges of Single-cell ATAC-seq.