scvi-tools vs Harmony
scvi-tools: Probabilistic deep generative models for single-cell omics (scVI, totalVI, scANVI...). Harmony: Fast, sensitive batch integration of single-cell data.
Facts below come from each project's own website, repository and paper. We don't publish benchmark claims here; see the papers for evaluations. Shared tags: integration.
| Field | scvi-tools | Harmony |
|---|---|---|
| Pretraining corpus | — | — |
| Architecture | Probabilistic generative models (VAE) | Iterative embedding correction |
| Tasks | Dimensionality reduction, integration, differential expression, annotation | Batch integration (~10^6 cells on a PC); scRNA + spatial |
| Species | — | — |
| License | BSD-3-Clause | GPL-3.0 |
| Pricing | Open source | Open source |
| Released | 2020-09-17 | 2018-11-04 |
| Paper | Link | Link |
| GitHub | GitHub | GitHub |
| GitHub stars | 1,713 | 677 |
| Interface | Package | Package |
License and commercial use
| Field | scvi-tools | Harmony |
|---|---|---|
| Code license | BSD-3-Clause | GPL-3.0 |
| Weights license | — | — |
| Commercial use | Permissive (commercial OK) | Copyleft (commercial OK, share-alike) |
| Answer | Yes. The recorded license is permissive, so closed-source commercial use is allowed if you keep the notices. Details | Yes, with conditions. It is under GPL: if you distribute modified or combined software, you must release the source under the same license. Details |
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