Release Notes

Version 1.0

1.3.1 2021-04-09

Bugfixes

• Fix estimator’s lineages color/names mismatch when reading from anndata.AnnData PR 556.

• Remove heuristics used to determine which solver to use PR 558.

1.3.0 2021-03-29

This release includes some major additions which make CellRank more applicable with and without RNA velocity information. In particular, it includes:

Additions

• 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 thresholding scheme inspired by [Setty et al., 2019], a soft thresholding 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:

  • Beyond RNA velocity: shows how to use CellRank when no RNA velocity information is available. PR 32

  • Creating a new kernel: explains how to create your own custom kernel class that estimates cell-cell transition probabilities PR 31.

• 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.

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.

1.2.0 2021-02-02

This release includes:

Additions

• Completely refactored the underlying code base of GPCCA and set it up as it’s own package called pyGPCCA with documentation and an example. Going forwards, this will ensure that one of the “engines” of CellRank is also easy to maintain to extend. Further, this will make CellRank’s installation more convenient by not needing to vendorize additional dependencies PR 472.

• Add cellrank.pl.circular_projection() visualizing computed fate probabilities as done in [Velten et al., 2017], see Plot circular embedding. PR 459.

• Allow legends not to be plotted by passing legend_loc="none", as done in scVelo PR 470.

Bugfixes

• Fix a bug when computing the Schur decomposition for reducible Markov chains (Schur vectors appear to not be D-orthogonal). GPCCA requires the leading Schur vectors to be orthogonal w.r.t. a symmetric, positive definite matrix \(D\) PR 453.

• Fix not falling back to mode='monte_carlo' if no jax is found when using mode='stochastic' in cellrank.tl.kernels.VelocityKernel.compute_transition_matrix() PR 472.

• Fix pandas v1.0.1 indexing error in cellrank.tl.lineage_drivers() PR 475.

• Fix not correctly propagating colors during aggregation in cellrank.tl.Lineage PR 482.

1.1.0 2020-11-17

This release includes:

Additions

• cellrank.tl.lineage_drivers() computes p-values for the identified driver genes now, using either a Fisher-transformation to approximate the distribution of the test statistic under the null hypothesis or an exact, permutation based test. Corrects for multiple-testing.

• cellrank.tl.kernels.VelocityKernel.compute_transition_matrix() now allows different metrics to be used to compare velocity vectors with expression-differences across neighboring cells. We add cosine-correlation and dot-product schemes and we allow the user to input their own scheme. It has been shown recently by [Li et al., 2021] that the choice of metric can lead to slightly different results. Users can now also supply their own scheme as long as it follows the signature of cellrank.tl.kernels.SimilaritySchemeABC.

• cellrank.datasets.reprogramming() has been added to allow for easy reproducibility of the time & memory benchmarking results in our CellRank preprint. This is a reprogramming dataset from [Biddy et al., 2018].

Bugfixes

• Fix not vendorizing correct msmtools which sometimes caused densification of a sparse matrix.

• Bump scanpy version requirement to 1.6 to fix plotting PR 444.

1.0.0 2020-10-17

• Fix a bug when subsetting cellrank.tl.Lineage

• Add renaming terminal states cellrank.tl.estimators.BaseEstimator.rename_terminal_states()

• Enable negative binomial distribution for cellrank.ul.models.GAMR

• Remove previously deprecated functions

• Add cellrank.ul.models.FailedModel inspired by the maybe monad

• Allow returning models when doing bulk fitting

• Add transpose parameter for cellrank.pl.gene_trends()

• Various minor bugfixes

1.0.0-rc.11 2020-09-25

• Rename final states to terminal states

• Fix pickling if cellrank.tl.estimators.BaseEstimator

• Fix various color bugs

• Improve cellrank.tl.kernels.PrecomputedKernel

• Update gallery

• Other various minor changes

1.0.0-rc.0 2020-07-15

• Fix pickling of cellrank.tl.Lineage

• Add additional options to cellrank.pl.heatmap()

• Updated documentation

1.0.0-b.8 2020-07-12

• Add installation options for PETSc and SLEPc

• Add iterative solver for absorption probabilities

• Add minor cellrank.tl.Lineage improvements

• Fix docstring issues

1.0.0-b.2 2020-07-02

• Fix installation by including future-fstrings

1.0.0-b.1 2020-07-02

• Initial beta pre-release