STABox: a one-stop platform for versatile spatial transcriptomics data analysis and three-dimensional visualization

• Installation
• Tutorial 1: 10x Xenium (human breast cancer FFPE tissues)
• Tutorial 2: Integrating Multi-slices
• Tutorial 3: Spatial domain-specific highly variable gene identification on human breast cancer FFPE tissues)
• Tutorial 4: STARmap PlUS
• Tutorial 5: Cell-type annotation on scST data
• Tutorial 6: Human brain M1 cells
• Tutorial 7: Download ST data from SODB and SpatialDB

Introduction

STABox is a one-stop platform for spatial transcriptomics data that provide a unified data processing pipeline, versatile data analysis modules, and interactive visualization. It integrates a suite of advanced analysis tools based on graph neural networks. STABox supports interactive 2D/3D visualization of spatial transcriptomics data, simplifying the generation and refinement of publication-ready high-quality images. STABox is extensible, allowing for seamless integration with various analysis methods to facilitate comprehensive downstream analysis of spatial transcriptomics data.

Manuscript

Please see our manuscript …