scMitoMut_paper_SUN_et_al

This repo contains the code for the paper "scMitoMut for calling mitochondrial lineage–related mutations in single cells" by SUN et al.

You can regenerate the results in the paper by running the scripts in this repo.

The instructions to prepare the data are provided in the README files in each subdirectory.

There are 8 subdirectories in this repo:

./lib/

It contains the specific version of the scMitoMut package used in this analysis.

This will be needed to run some of the scripts in the other directories.

./run_simu_multi_allele_per_locus/

Simulate multi-allele per locus data to evaluate the assumption of single-allele per locus in scMitoMut.

This analysis can be run without preparing the data.

./run_fitting_benchmark/

Benchmark the fitting performance of MLE (Beta-binomial model) and EM algorithms (Binomial-mixture model) in scMitoMut.

This analysis can be run without preparing the data.

./run_example_10xcnv/

Benchmark scMitoMut on 10x CNV data.

./run_example_crc/

Benchmark scMitoMut on CRC data.

./run_example_10x_brain/

Demo scMitoMut on 10x brain data.

./run_example_pbmc_granulocyte/

Demo scMitoMut on PBMC granulocyte data.