Moving to CellRank 2

The original CellRank version (v1) [Lange et al., 2022] was a framework to analyze cellular dynamics based on RNA velocity [Bergen et al., 2020, La Manno et al., 2018] and gene expression similarity. Based on a Markov chain formulation, it combined these two data modalities in a high-dimensional space and used the GPCCA algorithm [Reuter et al., 2022, Reuter et al., 2018] to compute initial and terminal states, fate probabilities, and driver genes.

With version 2, we are generalizing CellRank beyond RNA velocity data and turn it into a general framework for single-cell fate mapping based on various data modalities (see About CellRank). This required us to make substantial changes to CellRank’s API, many of which are backward-compatibility breaking. CellRank 2 can do everything that version 1 could do (and much more); however, it does it differently.


We outline the most important changes here. For a more detailed account, please refer to the Release Notes.

Important changes in version 2

There are many more changes and improvements in CellRank 2. For example, the computation of fate probabilities is 30x faster compared to version 1, we fixed many bugs, and improved and extended our documentation and tutorials.