spatial omics analysis pipeline

This release includes all scripts and documentation for analyzing spatial transcriptomics (Xenium) and proteomics (IMC) data from adult human ovary tissue. The code performs data preprocessing, clustering, visualization, differential gene/protein analysis, and spatial niche identification.

Compatible with:

Python 3.10 (Scanpy, CellCharter, Squidpy, matplotlib)
R 4.3 (cytomapper, ComplexHeatmap, imcRtools)
For full pipeline description, see README.md.