"CytoSimplex" is a Python module that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells. RNA velocity can be added as another layer of information.
For R users, we have an R package CytoSimplex that provides the same functionalities.
CytoSimplex can be installed with the shell/command-line command:
pip install cytosimplexWe have build a documentation website for:
- Detailed instruction for installation
- Walkthrough example from loading data to creating different simplex visualization
If you used CytoSimplex in your work, please cite the following work published on Bioinformatics:
Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2025, Bioinformatics, (https://doi.org/10.1093/bioinformatics/btaf119)