4 ms·
Python is catching up on single-cell transcriptomics; see AnnData, Scanpy, et al.
by flobosg 2y ago
Python is catching up on single-cell transcriptomics; see AnnData, Scanpy, et al.
- tetris11 2y agoScanPy/AnnData has been dead in the water for a while now, and most people use Seurat due to its operability with many many downstream extensions
- flobosg 2y ago> has been dead in the water for a while now Both are under active development and are used in several transcriptomics atlas projects, as far as I can tell.
- tetris11 2y agoThose 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
- valarauko 2y agoDisagree - 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
- _Wintermute 2y agoI have no dog in the Scanpy/Seurat argument, but AnnData is becoming very popular as a data format even outside of single-cell omics.