Single-Cell Mitochondrial Mutational burden analysis

Yu-Hsin Hsieh

This repository contains code needed to reproduce analyses and figures for the following work:

Hsieh et al., Single-cell multi-omics resolved analysis of mitochondrial genome-wide mutational burden, constraint, and mosaicism

• The POLG_HEK folder contains code for generating Figures 1-4 and Extended Data Figures 1-6.

    Fig1, Ext Fig1: 1_Preprocessing, 2_mtVAR_calling, 3_Mutational_Signature
  
    Ext Fig2: 7_ArchR, 7_ArchR_helperfunction
  
    Fig2, Ext Fig3: 2_mtVAR_visulization, 4_cor_mutNum_mtDepth
  
    Fig3, Ext Fig4: 6_VAF_dist_function, 6_VAF_dist_function
  
    Fig4, Ext Fig5-6: 8_scVAF, 5_1_scmtMMB, 5_2_scmtMMB_vis, 9_KI36_clonaltype
  

• The POLG_downsampling_analysis folder contains code for Extended Data Fig. 7

• The POLG_Galactose folder contains code for Figures 5 and Extended Data Fig. 8-9

• The PBMC folder contains code for generating Figures 6-7 and Extended Data Figures 10-12.

Due to GitHub's file size limitations, large data files (>100MB) are available from the Open Science Framework. Two zip archives are available: POLG_HEK_large_data_files.zip and PBMC_large_data_files.zip. After decompressing, locate the folder corresponding to the appropriate folder in the repository.