STmut

This release provides the first public version of STmut, a software toolkit developed in the Shain Laboratory for somatic mutation analysis in spatial transcriptomics data.

Characterizing gene expression profiles throughout tissue space provides key insights in investigating biological processes and disease development, including cancer. Bioinformatic tools exploring and interpreting spatial transcriptomics data are in great need - especially, approaches to visualize point mutations, allelic imbalance, and copy number variations (CNVs). CNVkit is a popular toolkit used to investigate the copy number alterations in both DNA-seq and RNA-seq data. Based on CNVkit-RNA and SAMtools, we provide an R package called stmut via this github page. The stmut package includes a series of functions to visualize copy number variations (CNVs), point mutations, and allelic imbalance in spatial transcriptomics data. We also provide the scripts producing the figures in the manuscript, which also serves as a user guide for this package. In addition, this package is also applicable to 10x single cell data analyses.

The functions in the stmut package are organized into 3 parts: CNVs, point mutations, and allelic imbalance.

This package was tested using R version 4.1.1, a macOS Monterey, Apple M1, 16G Memory. Given that spatial transcriptomics data normally have more than hundreds or thousands spots, we recommend using a high performance cluster to obtain point mutation and allelic imbalance for each spot.

STmut includes utilities for integrating somatic variant calls with spatial transcriptomics datasets, facilitating the identification and visualization of spatial patterns of mutation across tissue sections. The software supports standardized input formats for spatial gene expression and variant data, and is designed to work with pipelines for spatially resolved mutation analysis.

This initial release corresponds to the version of the code used in internal analyses of spatial somatic mutation distribution in sequencing and imaging datasets.

License: MIT License

Please cite the Zenodo DOI associated with this release when using this software in publications.

Changes in v1.0.0:

• Initial public release of STmut
• Tools for integration of somatic mutation calls with spatial transcriptomic data
• Documentation and example usage included