add citation info

Author: katosh

README.md

@@ -79,6 +79,22 @@ kompot de input.h5ad -o output.h5ad \
   - [Sample Variance Analysis](https://github.com/settylab/kompot/blob/main/examples/03_sample_variance.ipynb)
 - [CLI Guide](https://kompot.readthedocs.io/en/latest/cli.html)
 
+## Citation
+
+If you use Kompot in your research, please cite:
+
+```bibtex
+@article{Otto2025.06.03.657769,
+    author = {Otto, Dominik J. and Arriaga-Gomez, Erica and Thieme, Elana and Yang, Ruijin and Lee, Stanley C. and Setty, Manu},
+    title = {Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution},
+    year = {2025},
+    doi = {10.1101/2025.06.03.657769},
+    publisher = {Cold Spring Harbor Laboratory},
+    journal = {bioRxiv},
+    URL = {https://www.biorxiv.org/content/10.1101/2025.06.03.657769}
+}
+```
+
 ## License
 
 GNU General Public License v3 (GPLv3)

docs/source/index.rst

@@ -146,6 +146,30 @@ See the :doc:`CLI documentation <cli>` for complete usage and examples.
     Github Repo <https://github.com/settylab/kompot>
 
 
+Citation
+========
+
+If you use Kompot in your research, please cite:
+
+   Otto, D. J., Arriaga-Gomez, E., Thieme, E., Yang, R., Lee, S. C., & Setty, M. (2025).
+   Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution.
+   *bioRxiv*. https://doi.org/10.1101/2025.06.03.657769
+
+BibTeX:
+
+.. code-block:: bibtex
+
+   @article{Otto2025.06.03.657769,
+       author = {Otto, Dominik J. and Arriaga-Gomez, Erica and Thieme, Elana and Yang, Ruijin and Lee, Stanley C. and Setty, Manu},
+       title = {Comparing phenotypic manifolds with Kompot: Detecting differential abundance and gene expression at single-cell resolution},
+       year = {2025},
+       doi = {10.1101/2025.06.03.657769},
+       publisher = {Cold Spring Harbor Laboratory},
+       journal = {bioRxiv},
+       URL = {https://www.biorxiv.org/content/10.1101/2025.06.03.657769}
+   }
+
+
 Index
 =====