We used mouse brain data from the 10x Genomics Visium spatial transcriptomics platform (https://support.10xgenomics.com/spatial-gene-expression/datasets). We obtained the anterior1 slice with the SeuratData R package for this analysis29. The anterior1 slice consists of 31,053 genes and 2696 beads distributed in a 2D lattice. We used Seurat to normalize, obtain the 2D coordinates, and plot the spatial images. Genes with <10 beads with raw counts >1 were removed, resulting in 12,382 genes passing filtering. Raw counts were normalized with the NormalizeData function. Normalized counts and spatial coordinates were passed to the function haystack_2D to predict spatially differentially expressed genes, using a detection cutoff of 1.
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