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.