Single-cell chromatin state analysis with Signac

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Best practices for single-cell analysis across modalities (2023, methodology): “To identify potential CREs, correlation-based methods are used to link peaks to genes within clusters of cells 140,143,156 .”
Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “Thus, treating chromatin accessibility data as binary might be detrimental for downstream analyses 160,161 , and methods that handle accessibility in a quantitative manner might improve GRN reconstruction 154,155,162,163 .”
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays (2021, methodology): “Then, Signac (Stuart et al., 2021) was employed to analyze the scATAC-seq data using standard process.”