CellRank 1.3.0 (2021-03-29)#

Bugfixes#

  • Fix various bugs when plotting multiple gene trends PR 487.

  • Fix gene trend smoothing not working for 1 lineage PR 512.

  • Fix pandas error when computing macrostates PR 513.

  • Remove malfunctioning Edit on GitHub from the documentation PR 538.

Features#

  • Add new kernel cellrank.tl.kernels.CytoTRACEKernel which computes cell-cell transition probabilities based on the CytoTRACE score [Gulati et al., 2020], a measure of differentiation potential, PR 527.

  • Add external API cellrank.external with a stationary optimal transport kernel cellrank.external.kernels.OTKernel contributed from [Zhang et al., 2021], as well as a contributing guide, PR 522.

  • Rename cellrank.tl.kernels.PalantirKernel to cellrank.tl.kernels.PseudotimeKernel and add hard threshold scheme inspired by [Setty et al., 2019], a soft threshold scheme inspired by [Stassen et al., 2021] and a custom scheme when computing the transition matrix, see e.g. cellrank.tl.kernels.SoftThresholdScheme PR 514.

  • Add more flexibility to cellrank.tl.kernels.ConnectivityKernel, allowing it to use any cell-cell similarities from anndata.AnnData.obsp, such as spatial similarities from squidpy [Palla et al., 2021] PR 501.

  • Revamp Pancreas Advanced tutorial to showcase CellRank’s modular structure of kernels and estimators. PR 32.

  • Add 2 new tutorials:

  • Add projection of transition matrix onto an embedding cellrank.tl.kernels.Kernel.compute_projection()

  • Add random walk simulation and visualization in an embedding cellrank.tl.kernels.Kernel.plot_random_walks() PR 537.

  • Add cellrank.tl.Lineage.priming_degree() PR 502 which estimates a cell’s plasticity/differentiation potential based on ideas by [Setty et al., 2019] and [Velten et al., 2017].

  • Add checks for transition matrix irreducibility PR 516.

  • Add Zebrafish development dataset from [Farrell et al., 2018] PR 539.

  • Speed-up stationary distribution calculation in pygpcca PR 22.