Spatially Resolved Molecular Signatures of Lewy Body Dementia and the Impact of APOE4 This repository contains the computational methods used in the study: "Spatially resolved molecular signatures of Lewy body dementia and the Impact of APOE4" by Jin et al. This study investigates the spatial transcriptomic signatures of Lewy body dementia (LBD) with a focus on the impact of APOE4 genotype. Our analysis examines the molecular differences between APOE3 and APOE4 carriers in LBD patients. Code overview processAndIntegrate.r: QC, filtering, normalization and integration of spatial data using Seurat and Harmony. spacexrDeconvolution.r: Cell type deconvolution using SpaceXR. spacexr_functions.r: Custom extensions for SpaceXR. figures.R: Visualization scripts for all manuscript figures. dotplot_IPA.R: Visualization of Ingenuity Pathway Analysis results. upsetPlots.r: UpSet plots for differentially expressed gene intersections. stats.R: Statistical analysis of LB annotations across layers, genotypes, and disease states. Data Analysis Workflow The analysis follows these key steps: Processing and integration of spatial transcriptomics data Cell type deconvolution using snRNA-seq reference data Annotation of spatial spots for LB status and cortical layers Differential expression analysis between APOE genotypes Pathway analysis and visualization Contact Na Zhao (zhao.na@mayo.edu), Mayo Clinic, Department of Neuroscience for more information.