Table 1.
List of methods for cell cycle phase identification
| Name | Key features | Release date | Category | Language | Link |
|---|---|---|---|---|---|
| Oscope | Cyclic genes, pseudotime | 18 October 2015 | Marker genes–based clustering | R | https://www.biostat.wisc.edu/~kendzior/OSCOPE/ |
| cyclone | Cell cycle phase | 9 December 2015 | Marker genes–based clustering | R | https://rdrr.io/bioc/scran/man/cyclone.html |
| ccRemover | Remove cell cycle | 19 August 2017 | Marker genes–based clustering | R | https://github.com/cran/ccRemover |
| f-scLVM | Cyclic genes, remove cell cycle | 11 November 2017 | Marker genes–based clustering | Python, R | https://github.com/scfurl/f-scLVM |
| cycleX | Cell cycle phase, pseudotime | 20 November 2017 | Marker genes–based clustering | Python, R | workflow |
| reCAT | Cell cycle phase, cyclic genes, g0, pseudotime | 16 March 2019 | Marker genes–based clustering | R | https://github.com/tinglab/reCAT |
| Pre-Phaser | Cell cycle phase, g0, pseudotime | 6 September 2019 | Machine learning | C++, Python | https://github.com/ayurovsky/Pre-Phaser |
| CCPE | Cell cycle phase, cyclic genes, high dimensional, pseudotime, remove cell cycle | 6 January 2021 | Marker genes–based clustering | Matlab, Python, R | https://github.com/LiuJJ0327/CCPE |
| Cyclum | Cell cycle phase, cyclic genes, pseudotime, remove cell cycle | 18 March 2020 | Machine learning | Python | https://github.com/KChen-lab/Cyclum |
| DeepCycle | Cell cycle phase, cyclic genes, deep learning, pseudotime | 29 July 2021 | Machine learning | Python | https://github.com/andreariba/DeepCycle |
| ccAF | Cell cycle phase, g0, machine learning | 14 May 2020 | Machine learning | Python | https://github.com/plaisier-lab/ccAF |
| peco | Continuum, cyclic genes, pseudotime | 13 November 2020 | Machine learning | R | https://github.com/jhsiao999/peco |
| tricycle | Cell cycle phase, cyclic genes, pseudotime, remove cell cycle, transfer learning | 18 March 2022 | Machine learning | R | https://github.com/hansenlab/tricycle |
| Seurat | Cell cycle phase, remove cell cycle, score | 27 June 2018 | Marker genes–based clustering | Python, R | https://satijalab.org/seurat/articles/cell_cycle_vignette.html |
| Revelio | Cell cycle phase, cyclic genes, pseudotime, remove cell cycle | 1 November 2020 | Marker genes–based clustering | R | https://github.com/danielschw188/Revelio |
| CSICC | Cell cycle phase, g0, pseudotime | 12 May 2022 | Marker genes–based clustering | R, Web | https://sc1.engr.uconn.edu |