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CytoSimplex is an R package 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 Python users, we have a Python package CytoSimplex that provides the same functionalities.


The package is developed and tested under R>=4.2.0. Users can install R following the instruction provided on CRAN. RStudio is a recommended IDE for working with R projects.

To install CytoSimplex in R, run the following command in an R console:


For the latest developmental version, run the following command in an R console:

if (!requireNamespace("devtools", quietly = TRUE))


We have created a documentation website for posting example tutorials walking through the process from loading the provided example data and creating different types of visualization.