Table 3.
List of methods compared in the benchmark.
| Method | Version | Class of clustering technique | Publication |
|---|---|---|---|
| ascend | v0.9.0 | Hierarchical | Senabouth et al. (2019) |
| CIDR | v0.1.5 | Hierarchical | Lin et al. (2017) |
| DIMMSC | v0.2.1 | Model-based | Sun et al. (2018) |
| Linnorm | v2.6.1 | Partitioning | Yip et al. (2017) |
| monocle3 | v2.99.2 | Multiple choices | Qiu et al. (2017) |
| pcaReduce | v1.0 | Hierarchical | Zurauskiene and Yau (2016) |
| RaceID3 | v0.1.3 | Multiple choices | Herman and Grün (2018) |
| SC3 | v1.10.1 | Partitioning | Kiselev et al. (2017) |
| Seurat | v2.3.4 | Graph-based | Macosko et al. (2015) |
| SIMLR | v1.8.1 | Partitioning | Wang et al. (2017) |
| sincell | v1.14.1 | Multiple choices | Julia et al. (2015) |
| sscClust | v0.1.0 | Multiple choices | Ren et al. (2019) |
| TSCAN | v1.20.0 | Model-based | Ji and Ji (2016) |
Versions of the R packages (methods) compared in this study. Methods are based on various clustering techniques that can be categorized based on the cluster-model. Multiple choices indicate that the method allows to cluster cells with more than one clustering technique.