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| 1 | <img src="https://github.com/Lotfollahi-lab/nichecompass/blob/main/docs/_static/nichecompass_logo_readme.png" width="800" alt="nichecompass-logo"> |
1 | <img src="https://github.com/Lotfollahi-lab/nichecompass/blob/main/docs/_static/nichecompass_logo_readme.png?raw=true" width="800" alt="nichecompass-logo"> |
| 2 | 2 | ||
| 3 | [](https://github.com/Lotfollahi-lab/nichecompass/blob/main/LICENSE) |
3 | [](https://github.com/Lotfollahi-lab/nichecompass/blob/main/LICENSE)
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| 4 | [](https://github.com/Lotfollahi-lab/nichecompass/stargazers) |
4 | [](https://github.com/Lotfollahi-lab/nichecompass/stargazers)
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| 5 | [](https://pypi.org/project/nichecompass) |
5 | [](https://pypi.org/project/nichecompass)
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| 6 | [](https://pepy.tech/project/nichecompass) |
6 | [](https://pepy.tech/project/nichecompass)
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| 7 | [](https://nichecompass.readthedocs.io/en/stable/?badge=stable) |
7 | [](https://nichecompass.readthedocs.io/en/stable/?badge=stable)
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| 8 | [](https://github.com/psf/black) |
8 | [](https://github.com/psf/black)
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| 9 | [](https://github.com/pre-commit/pre-commit) |
9 | [](https://github.com/pre-commit/pre-commit) |
| 10 | 10 | ||
| 11 | 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/). |
11 | 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/). |
| 12 | 12 | ||
| 13 | ## Resources |
13 | ## Resources
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| 14 | - An installation guide, tutorials and API documentation is available in the [documentation](https://nichecompass.readthedocs.io/). |
14 | - An installation guide, tutorials and API documentation is available in the [documentation](https://nichecompass.readthedocs.io/).
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| 15 | - Please use [issues](https://github.com/Lotfollahi-lab/nichecompass/issues) to submit bug reports. |
15 | - Please use [issues](https://github.com/Lotfollahi-lab/nichecompass/issues) to submit bug reports.
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| 16 | - If you would like to contribute, check out the [contributing guide](https://nichecompass.readthedocs.io/en/latest/contributing.html). |
16 | - If you would like to contribute, check out the [contributing guide](https://nichecompass.readthedocs.io/en/latest/contributing.html).
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| 17 | - If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript. |
17 | - If you find NicheCompass useful for your research, please consider citing the NicheCompass manuscript. |
| 18 | 18 | ||
| 19 | ## Reference |
19 | ## Reference
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| 20 | ``` |
20 | ```
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| 21 | @article{Birk2025, |
21 | @article{Birk2025,
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| 22 | author = {Birk, S. and Bonafonte-Pard{\`a}s, I. and Feriz, A. M. and et al.}, |
22 | author = {Birk, S. and Bonafonte-Pard{\`a}s, I. and Feriz, A. M. and et al.},
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| 23 | title = {Quantitative characterization of cell niches in spatially resolved omics data}, |
23 | title = {Quantitative characterization of cell niches in spatially resolved omics data},
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| 24 | journal = {Nature Genetics}, |
24 | journal = {Nature Genetics},
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| 25 | year = {2025}, |
25 | year = {2025},
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| 26 | doi = {10.1038/s41588-025-02120-6}, |
26 | doi = {10.1038/s41588-025-02120-6},
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| 27 | url = {https://doi.org/10.1038/s41588-025-02120-6} |
27 | url = {https://doi.org/10.1038/s41588-025-02120-6}
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| 28 | } |
28 | }
|
| 29 | ``` |
29 | ```
|