In a higher-eukaryotes organism, each organ contains multiple cell types in a highly organized manner. A fundamental biological question is how cells interact with each other to coordinate the function of the entire organ. The recent development of spatial transcriptomics technologies has provided an unprecedented opportunity to systematically investigate the structural organization at single-cell resolution, yet it has also presented a number of new challenges for data analysis and interpretation. In the past few years, our lab has developed a number of computational methods for cell-type deconvolution, spatial domain identification, and ligand-receptor analysis. We have further developed Giotto as a generally applicable, comprehensive pipeline for spatial transcriptomics analysis. In this talk, I will give an introduction to these tools.