Spatial Transcriptome Analysis

Package Overview

Goal

Analysis of spatial transcriptome data (seq-based or in-situ)

Requirements

• Spatial datasets with at least 100 cells
• Technologies 10x Visium and 10x Xenium
• Replicates recommended for identification of differentially expressed genes

Analysis

• Mapping and counting (Space Ranger for 10x Visium, Xenium Ranger for 10x Xenium)
• Quality control, filtering of low quality cells and normalization
• Multi-sample integration and batch effect removal
• Clustering and visualization
• Identification and functional annotation of marker genes
• Analysis of cell composition differences
• Identification of differentially expressed genes
• Visualization in spatial context and identification of spatially important genes

Output

• Mapped sequence data and counts
• Extensive HTML report with plots, tables and documentation
• Result files for further analysis (Excel, R, CSV)
• Files for interactive exploration of the data (Loupe/Xenium Explorer and cellxgene)

Advanced Analysis

• Improved cell segmentation
• Identification of cell-types based on existing single-cell datasets (provided counts and cell type annotation are available)
• Niche analyses
• Identification of spatial structures