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Analysis for immune pan-cancer snATAC project

  1. 1.GRN_analysis -- scripts for gene regulatory network (GRN) analysis using SCENIC.

  2. 2.Monocle_multiome -- scripts for running monocle analysis using multiome object. Note: we used ATAC assay as input for monocle2, and then use inferred pseudotime scores for the subsequent analysis.

  3. 3.Monocle_results_plotting -- scripts for plotting monocle2 results for regulons and DEGs.