Protocol to decipher complex spatial transcriptomics data using STMiner

Complex spatial transcriptomics (ST) data analysis can be challenging due to uneven sampling, sparsity, and ambiguous tissue boundaries. Here, we present a protocol for deciphering complex ST data using STMiner. We describe steps for installing STMiner, loading ST data into STMiner, and identifying spatially variable genes. We then detail procedures for determining gene sets associated with the structure of interest and obtaining spatial expression patterns. This protocol can be applied to varying resolutions and platforms, without additional reference data. For complete details on the use and execution of this protocol, please refer to Sun et al.¹.