# Documentation

NicheCompass (**N**iche **I**dentification based on **C**ellular grap**H** **E**mbeddings of **COM**munication **P**rograms **A**ligned across **S**patial **S**amples) 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](https://pytorch-geometric.readthedocs.io/en/latest/) and [AnnData](https://anndata.readthedocs.io/en/latest/).

The package is developed and maintained by the [Lotfollahi Lab](https://github.com/Lotfollahi-lab) at the Wellcome Sanger Institute.

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:::{grid-item-card} Installation {octicon}`plug;1em;`

:link: installation

:link-type: doc

Check out the installation guide.

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:::{grid-item-card} Tutorials {octicon}`play;1em;`

:link: tutorials/index

:link-type: doc

Learn by following example applications of NicheCompass.

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:::{grid-item-card} User Guide {octicon}`book;1em;`

:link: user_guide/index

:link-type: doc

Review good practices for training NicheCompass models on your own data.

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:::{grid-item-card} API {octicon}`info;1em;`

:link: api/index

:link-type: doc

Find a detailed description of NicheCompass APIs.

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:::{grid-item-card} Release Notes {octicon}`tag;1em;`

:link: release_notes/index

:link-type: doc

Follow the latest changes to NicheCompass.

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:::{grid-item-card} Contributing {octicon}`code;1em;`

:link: contributing

:link-type: doc

Help improve NicheCompass.

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If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript.

```{toctree}

:hidden: true

:maxdepth: 3

:titlesonly: true

installation

tutorials/index

api/index

release_notes/index

contributing.md

references.md

```