We offer pre-processing of data from 10x Genomics Visium spatial gene expression assays. We use spaceranger count to perform fiducial detection, map the reads to the reference genome and count the number of reads overlapping with each gene to produce a count matrix for each sample. After that, we perform downstream analyses with the R package Seurat, and others, resulting in quality control, transformation, clustering, differential gene expression, automatic cell-type annotation, spatial variable gene identification, cluster neighborhood analyses, cell-type deconvolution and visualizations.
