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Those atlases were established back when Scanpy and Seurat were relatively beta and were still fighting out the tool space.

Look at the packages now for integration, pseudo time, pseudobulk - R (and therefore Seurat) dominates heavily

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Disagree - Seurat had first mover advantage with single cell but sucked with larger datasets that Scanpy could handle till the big change in Seurat 5. The preference for either Seurat/Scanpy is incredibly lab specific. That said, Seurat is better documented for sure, but the ecosystem for both is incredibly rich and flourishing.

yeah, I also disagree with this. It's true Seurat is still heavily used for scRNA/scATAC but I see most new models increasingly being written/tooled for python and based on anndata. Geneformer, scGPT, scVI etc. I wish there was better operability between the scverse stuff and Seurat, but Seurat went their own way from SCE/bioconductor so that's probably not going to happen.

To be fair to them, getting anything submitted to buoconductor requires a ton of effort, and the pay off is often less concise code

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