Table 1. Comparison of single-cell visualization tools.
| Pagoda | Cerebro | Single Cell Viewer | CellexalVR | Cellxgene | Single Cell Portal | ScelVis | |
|---|---|---|---|---|---|---|---|
| Reference | Fan et al. (2016) | Hillje, Pelicci & Luzi (2019) | Wang et al. (2019) | Legetth et al. (2018) | chanzuckerberg. github.io/ cellxgene/ | singlecell. broadinstitute.org | This study |
| Version | v0.1.1 | v1.1.0 | v0.13.0 | v0.13.0 | v0.38.0 | v0.8.1 | |
| Language | R | R | R | C# | Python | ruby | Python |
| Platform | Browser | Browser | Browser | Windows 10 | Browser | Browser | Browser |
| License | GPL-3.0 | MIT | GPL-3.0 | GPL-3.0 | MIT | BSD 3-clause | MIT |
| Additional dependencies | None | None | None | HTC Vive Controller | None | Google Cloud Platform etc. | None |
| Plot types | Scatter, heatmap | Scatter, violin, heatmap, box, bar | Scatter, heatmap, dot | Scatter, heatmap | Scatter, histogram | Scatter, violin, heatmap, box | Scatter, violin, box, bar, dot |
| Cell filtering | ✓ | ✓ | ✓ | ✓ | ✓ | × | ✓ |
| Differential expression | ✓ | ✓ | ✓ | ✓ | ✓ | × | ✓ |
| Data input | Local + remote | Local | Local | Local | Local + remote | Local + remote | Local + remote |
| Input formats | Pagoda | Seurat | Seurat | Raw | Anndata | raw | Anndata, loom, raw, CellRanger |
| Conversion | × | ✓ | × | ✓ | ✓ | ✓ | ✓ |