Import CellRank as:

import cellrank as cr

CellRank has a modular API, organized around kernels and estimators:

  • Kernels compute cell-cell transition matrices using various input data modalities, including RNA velocity, any pseudotime, a developmental potential, experimental time points, and more.

  • Estimators use the cell-cell transition matrix to derive insights about cellular dynamics, for example, they compute initial and terminal states, fate probabilities, and driver genes. Our recommended estimator is cellrank.estimators.GPCCA.

  • In addition, there are models for gene trend fitting, plotting functions for visualization, and datasets that help you getting started with CellRank.

If you are new to CellRank, check out our about CellRank page, and take a look at our tutorials.