I have hands-on experience working on a spatial transcriptomics project involving brain tissue sections from Alzheimer’s disease patients. Throughout this project, I implemented a complete end-to-end analysis pipeline, beginning with raw data quality control and preprocessing using SpaceRanger. Conduction of downstream data integration, normalization, and spatial quality control using Seurat, ensuring robust handling of the spatial gene expression matrices. For cell type annotation, I utilized both scCATCH and scType, enabling high-confidence mapping of transcriptional profiles to known cell populations. To interrogate transcriptional changes, performing of  pseudobulk differential expression analysis, complemented by fine-grained marker detection using Seurat’s FindMarkers function. Spatial deconvolution was achieved using SPOTlight, providing insights into the cellular composition of spatial spots. Furthermore, cell-cell communication analysis was performed using CellChat, uncovering interaction networks potentially perturbed in disease states. This comprehensive experience has strengthened my proficiency in spatial transcriptomics workflows and the application of advanced computational tools in spatial omics.