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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 prefe
by valarauko 2y ago
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.
- cd4plus 2y agoyeah, 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.
- tetris11 2y agoTo be fair to them, getting anything submitted to buoconductor requires a ton of effort, and the pay off is often less concise code