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 varyi...

STMiner considers the impact of uneven sampling in spatial transcriptomics data on downstream analyses, enabling effective identification of genes with spatial characteristics and their spatial expres...