README.md

CytoSimplex

"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 cytosimplex

We 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:

Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2023, bioRxiv