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.
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:::{grid-item-card} Installation {octicon}plug;1em;
🔗 installation
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Check out the installation guide. :::
:::{grid-item-card} Tutorials {octicon}play;1em;
🔗 tutorials/index
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Learn by following example applications of NicheCompass. :::
:::{grid-item-card} API {octicon}info;1em;
🔗 api/index
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Find a detailed description of NicheCompass APIs. :::
:::{grid-item-card} Release Notes {octicon}book;1em;
🔗 release_notes/index
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Follow the latest changes to NicheCompass. :::
:::{grid-item-card} Contributing {octicon}code;1em;
🔗 contributing
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Help improve NicheCompass. ::: ::::
If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.
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installation
tutorials/index
api/index
release_notes/index
contributing.md
references.md