Single-cell chromatin accessibility analysis enables high-resolution dissection of regulatory elements and gene regulatory mechanisms. However, standardized and comprehensive analysis workflows remain limited. In this study, we present a streamlined pipeline for analyzing single-cell chromatin accessibility data. The workflow begins with data preprocessing using single-cell assay for transposase-accessible chromatin (scATAC)-pro or Cell Ranger ATAC, followed by peak calling with MACS2 and differential accessibility analysis to detect open chromatin regions and perform differential accessibility analysis to highlight regulatory differences among cell populations. Transcription factor activity is then inferred using chromVAR, incorporating motif enrichment and footprinting analysis. Finally, SCENIC+ is applied to reconstruct transcriptional regulatory networks, enabling in-depth exploration of epigenetic mechanisms at the single-cell level. This integrative approach offers a robust framework for decoding the regulatory landscape and understanding cellular heterogeneity in complex biological systems.
Zhang et al. (2026) studied this question.