ATLAS - Advanced Trajectory Learning from multi-omics At Single-cell resolution

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:

 <diff.cif.fraction>_<cif.sigma>_spliced.tsv 

<diff.cif.fraction>_<cif.sigma>_unspliced.tsv 

<diff.cif.fraction>_<cif.sigma>_atac.tsv 

<diff.cif.fraction>_<cif.sigma>_activity.tsv 

<diff.cif.fraction>_<cif.sigma>_metadata.tsv