Documentation
NicheCompass (Niche Identification based on Cellular grapH Embeddings of COMmunication Programs Aligned across Spatial Samples) is a package for end-to-end analysis of spatial multi-omics data, including spatial atlas building, niche identification & characterization, cell-cell communication inference and spatial reference mapping. It is built on top of PyG and AnnData. The package is developed and maintained by the Lotfollahi Lab at the Wellcome Sanger Institute.
If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.