To build the cell population gene regulatory network, we used LINGER, as described in Yuan & Duren, 2024.43 We generated pseudobulk-level expression and chromatin accessibility data for each donor and each cell type. Here we used the union set of peaks (described above) for ATAC-seq data. as well as a covariate matrix, with 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.
