To build the cell population gene regulatory network, we used LINGER40. We generated pseudobulk-level expression and chromatin accessibility data for each donor and each cell type. Here, we used the union set of peaks across all cell types (described above) for ATAC-seq data and sex, age, and ethnic origin as covariates to the model. All samples used for differential accessibility testing (see “ATAC pseudobulk samples creation”) were used for this analysis.
