Citing CellRank

If you find CellRank useful for your research, please consider citing our work as follows: If you are using CellRank’s VelocityKernel with classical RNA velocity, cite [Lange et al., 2022] as:

    title = {CellRank for directed single-cell fate mapping},
    author = {Lange, Marius and Bergen, Volker and Klein, Michal and Setty, Manu and
              Reuter, Bernhard and Bakhti, Mostafa and Lickert, Heiko and
              Ansari, Meshal and Schniering, Janine and Schiller, Herbert B. and
              Pe'er, Dana and Theis, Fabian J.},
    journal = {Nat. Methods},
    year = {2022},
    doi = {10.1038/s41592-021-01346-6},
    publisher = {Nature Publishing Group}

If you are using the PseudotimeKernel, CytoTRACEKernel, RealTimeKernel, or the VelocityKernel with velocities inferred from metabolic labeling data using the CellRank 2 approach, cite [Weiler et al., 2023] as:

    title = {Unified fate mapping in multiview single-cell data},
    author = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe{\textquotesingle}er, Dana and Theis, Fabian},
    doi = {10.1101/2023.07.19.549685},
    url = {},
    year = {2023},
    publisher = {Cold Spring Harbor Laboratory},

In addition, if you use the GPCCA estimator to compute initial, terminal or intermediate states, you are using the pyGPCCA package [Reuter et al., 2022] under the hood, which implements the Generalized Perron Cluster Cluster Analysis (GPCCA) algorithm. Thus, additionally to CellRank, please cite GPCCA [Reuter et al., 2019] as:

    author = {Reuter,Bernhard  and Fackeldey,Konstantin  and Weber,Marcus },
    title = {Generalized Markov modeling of nonreversible molecular kinetics},
    journal = {The Journal of Chemical Physics},
    volume = {150},
    number = {17},
    pages = {174103},
    year = {2019},
    doi = {10.1063/1.5064530},