End-to-end analysis of spatial multi-omics data
Project description
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.
Resources
- An installation guide, tutorials and API documentation is available in the documentation.
- Please use issues to submit bug reports.
- If you would like to contribute, check out the contributing guide.
- If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.
Reference
@article{Birk2024Quantitative,
title = {Quantitative characterization of cell niches in spatial atlases},
author = {Birk, S. and others},
journal = {bioRxiv},
year = {2024},
doi = {10.1101/2024.02.21.581428},
url = {https://www.biorxiv.org/content/10.1101/2024.02.21.581428}
}
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