10x Genomics Xenium In Situ Gene and Protein Expression data (FFPE Human Renal Cell Carcinoma) for DiagVI Tutorial

10x Xenium in situ gene and protein expression dataset (from https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma) profiling a FFPE human renal cell carcinoma sample.The dataset was downloaded from 10x Genomics and the following processing steps have been applied:aggregating protein intensities over provided cell segmentation masksbasic single-cell analysis (calculating quality control metrics, filtering cells and genes, dimensionality reduction, clustering)correcting (by subtracting background offset) and clipping protein intensitieshierarchical cell type annotation based on differentially expressed marker genes and Leiden clusteringsplitting of dataset into two separate AnnData objects to artificially decouple the gene and protein measurements by treating them as originating from independent cellsThe resulting dataset consists of one AnnData object containing RNA measurements (395,161 cells × 405 genes) and one AnnData object containing protein measurements (395,161 cells × 23 proteins). The dataset is used as a ground truth dataset for the development of DiagVI, a deep generative model for integrating unpaired multi-modal single-cell data using prior biological knowledge encoded in a guidance graph.