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README.md

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 Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale.
 Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
 
-**See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)**  
+**See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/)**  
+
+**Panpipes is on [Genome Biology!](https://link.springer.com/article/10.1186/s13059-024-03322-7)**
 
 These workflows make use of [cgat-core](https://github.com/cgat-developers/cgat-core)
 
@@ -53,9 +55,9 @@ Check the example [submission file](https://github.com/DendrouLab/panpipes/blob/
 
 ## Citation
 
-[Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
-Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Tom Thomas, Fabian J. Theis, Calliope A. Dendrou
-bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)
+[Curion, F., Rich-Griffin, C., Agarwal, D. et al. Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis. Genome Biol 25, 181 (2024). 
+doi: https://doi.org/10.1186/s13059-024-03322-7](https://link.springer.com/article/10.1186/s13059-024-03322-7)
+
 
 ## Contributors