scMutrace Tutorial

A complete beginner’s guide to learning scMutrace from scratch, including both example and application projects.

Contents

• Preprocessing Steps (preProcessingSteps folder. Reproducible workflows used in the scMutrace paper)
• Example Projects (QuickStart folder. Step-by-step demonstrations to help you understand the basics)
• Reproducibility Code(ReproducibilityAnalysis folder. Practical use cases from our paper to reproduce our results)
• Other Functions (OtherFunctions folder. Explore extended features and customization options)

If you encounter coding issues along the way, you can refer to the shell script examples provided here:

https://github.com/QunATCG/shell-scripting-tutorial

https://github.com/QunATCG/linux-command

https://github.com/QunATCG/scMutrace

If you have any questions or encounter problems, please open an issue here: scMutrace-tutorial Issues

Or contact us: qun.li@ki.se and claudia.kutter@ki.se

Resources

• COSMIC and 1000 Genomes–Based Mutation Annotation https://doi.org/10.5281/zenodo.16925906

• Databases for scMutrace Calling (generated from public databases)

  Zenodo: https://doi.org/10.5281/zenodo.16962722

  Google Drive (mirror): https://drive.google.com/file/d/18DEmJ2CbmFV7vpADlLIxdHVpxw31DTWI/view?usp=drive_link

Citing scMutrace

License

MIT License

References

Muyas F. et al. De novo detection of somatic mutations in high-throughput single-cell profiling data sets. Nature Biotechnology. (2024)

Dou J. et al. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nature Biotechnology. (2024).

The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. (2015)

Zbyslaw Sondka. et al. COSMIC: a curated database of somatic variants and clinical data for cancer. Nucleic Acids Research. (2024)

Perez G. et al. The UCSC Genome Browser database: 2025 update. Nucleic Acids Research. (2025)

Karczewski K.J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. (2020)

Mansi L. et al. REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments. Nucleic Acids Research. (2021)