This repository contains sythetic data generated in ATLAS (Advanced Trajectory Learning from multi-omics At Single-cell resolution). Data were generated using scMultiSim v1.0.0 and R v4.4.1. True transcript and chromatin-accessibility counts were generated with the sim_true_counts function, using the built-in 100-genes GRN (GRN_params_100) and both three- and five-branches differentiation trees (Phyla3 and Phyla5) and multiple values for the cif.sigma and the diff.cif.fraction parameters. Data are structured in sub-folders according to the differentiation tree. simulated_data - three_branches - five_branches Within each sub-folder, data files follows the following naming conventions: __spliced.tsv __unspliced.tsv __atac.tsv __activity.tsv __metadata.tsv