File description:

SSV_full_analysis_V1.R: Code for the identification and analysis of subpopulation-specific variants (SSVs) in simulated data.
SSV_simulation_sample_run.sh: An example script for running the SSV analysis in simulated data.
SSV_PBMC_Old_Young.ipynb: Code for the identification and analysis of SSVs of PBMC samples from young and old donors.
SSV_HSPC_colonies_Ludwig.ipynb: Code for the identification and analysis of SSVs of HSPC-derived colonies.
SSV_T_cells_Zhang.ipynb: Code for the identification and analysis of SSVs of T cells isolated from CRC patients.
SSV_T_cells_Li.ipynb: Code for the identification and analysis of SSVs of T cells isolated from autoimmune diseases.
