Import CellRank as:

import cellrank as cr

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

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

  • cellrank.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 the GPCCA estimator.

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