Codes used for benchmarking scMINER in cell clustering, network inference and hidden driver identification
network_inference/ATAC_GRN_evaluation - evaluation of TF network based on ATAC-Seq data. Required input: expression tables, networks inferred with scMINER, GENIE3, GRNBoost2 and PIDC, list of TFs and SIGs
network_inference/CROP_Seq_GRN_evaluation - evaluation of TF and SIG networks based on CROP-Seq data. Required input: expression tables (single-cell and metacell), networks inferred with scMINER, GENIE3, GRNBoost2 and PIDC, list of TFs and SIGs, activity matrix.
activity_estimation/PBMC - analysis of PBMC dataset.
activity_estimation/TEX - analysis of exhausted T-cells dataset.
activity_estimation/Tregs - analysis of regulatory T-cells dataset.
Required input: Expression table, activity matrix computed with scMINER and with SCENIC, clustering results obtained with MICA.