CellRank 1.4.0 (2021-06-30)


  • Fix estimator’s inconsistent state when reading from anndata.AnnData PR 563.

  • Fix not checking whether probabilities sum to 1 in cellrank.tl.estimators.BaseEstimator.compute_absorption_probabilities() PR 566.

  • Fix always forcing sparse transition matrix in cellrank.tl.kernels.Kernel PR 586.

  • Fix passing custom connectivity key in cellrank.tl.kernels.Kernel PR 590.

  • Fix kernels in cellrank.external always requiring connectivities PR 600.

  • Fix parallelization of sparse matrix with too many jobs PR 633.

  • Fix plotting coarse-grained transition matrix when no stationary distribution is found Issue 594.


  • Add new external kernel based on Waddington optimal transport [Schiebinger et al., 2019] cellrank.external.kernels.WOTKernel PR 595.

  • Add new tutorial Time series datasets that shows how to use the external Waddington OT kernel PR 35.

  • Add reprogramming dataset cellrank.datasets.reprogramming_schiebinger() from [Schiebinger et al., 2019] PR 631.

  • Add cellrank.pl.log_odds() to plot log-odds ratio between 2 lineages sorted by experimental time. PR 642.

  • Add cellrank.tl.estimators.GPCCA.plot_macrostate_composition() to visualize macrostate composition over a categorical variable PR 641.

  • Add cellrank.tl.estimators.BaseEstimator.plot_lineage_drivers_correlation() to plot lineage driver correlation with 2 lineages in a scatter plot PR 640.

  • Add cellrank.tl.kernels.Kernel.plot_single_flow() based on [Mittnenzweig et al., 2021] to visualize outgoing transition matrix flow in clusters across experimental time PR 615.

  • Dramatically speed-up the computation of fate probabilities (>5x) PR 638.

  • Remove 4 technical examples and add 2 new examples PR 602:

    • projection of transition matrix onto an embedding.

    • simulation of random walks on a Markov chain.

  • Add option to visualize cell-level covariates in cellrank.pl.cluster_lineage() PR 634.

  • Add option to force-recompute transition matrix in cellrank.tl.initial_states() and cellrank.tl.terminal_states() PR 577.

  • Change cellrank.tl.kernels.PseudotimeKernel defaults and prune available parameters of soft threshold scheme PR 583.

  • Parallelize transition matrix computation in cellrank.tl.kernels.PseudotimeKernel PR 587.

  • Prune requirements.txt PR 571.

  • Add small improvements to documentation PR 584 PR 601 PR 605 PR 648.