Table 5
Methods for single-cell trajectory inference.
Tools | Dimensionality reduction | URL | References |
---|---|---|---|
Monocle | ICA | http://cole-trapnell-lab.github.io/monocle-release/ | Trapnell et al., 2014 |
Waterfall | PCA | https://www.cell.com/cms/10.1016/j.stem.2015.07.013/attachment/3e966901-034f-418a-a439-996c50292a11/mmc9.zip | Shin et al., 2015 |
Wishbone | Diffusion maps | https://github.com/ManuSetty/wishbone | Setty et al., 2016 |
GrandPrix | Gaussian Process Latent Variable Model | https://github.com/ManchesterBioinference/GrandPrix | Ahmed et al., 2019 |
SCUBA | t-SNE | https://github.com/gcyuan/SCUBA | Marco et al., 2014 |
DPT | Diffusion maps | https://media.nature.com/original/nature-assets/nmeth/journal/v13/n10/extref/nmeth.3971-S3.zip | Haghverdi et al., 2016 |
TSCAN | PCA | https://github.com/zji90/TSCAN | Ji and Ji, 2016 |
Monocle2 | RGE | http://cole-trapnell-lab.github.io/monocle-release/ | Qiu et al., 2017 |
Slingshot | Any | https://github.com/kstreet13/slingshot | Street et al., 2018 |
CellRouter | Any | https://github.com/edroaldo/cellrouter | Lummertz da Rocha et al., 2018 |