Scanpy vs Seurat
Scanpy: Scalable Python toolkit for single-cell gene expression analysis. Seurat: R toolkit for single-cell genomics, integration and multimodal analysis.
Facts below come from each project's own website, repository and paper. We don't publish benchmark claims here; see the papers for evaluations.
| Field | Scanpy | Seurat |
|---|---|---|
| Pretraining corpus | N/A (analysis toolkit, no pretraining) | — |
| Architecture | Python toolkit built on AnnData | — |
| Tasks | General analysis (>1M cells) | Integration incl. cross-modality bridge integration, multimodal analysis |
| Species | — | Human, mouse, others |
| License | BSD-3-Clause | MIT |
| Pricing | Open source | Open source |
| Released | 2017-08-09 | 2015-04-13 |
| Paper | Link | Link |
| GitHub | GitHub | GitHub |
| GitHub stars | 2,590 | 2,805 |
| Interface | — | — |
License and commercial use
| Field | Scanpy | Seurat |
|---|---|---|
| Code license | BSD-3-Clause | MIT |
| Weights license | — | — |
| Commercial use | Permissive (commercial OK) | Permissive (commercial OK) |
| Answer | Yes. The recorded license is permissive, so closed-source commercial use is allowed if you keep the notices. Details | Yes. The recorded license is permissive, so closed-source commercial use is allowed if you keep the notices. Details |
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