This release includes:
Fix not vendorizing correct
msmtoolswhich sometimes caused densification of a sparse matrix.
Bump scanpy version requirement to 1.6 to fix plotting PR 444.
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 [Li2020] 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
Fix a bug when subsetting
Add renaming terminal states
Enable negative binomial distribution for
Remove previously deprecated functions
cellrank.ul.models.FailedModelinspired by the maybe monad
Allow returning models when doing bulk fitting
Various other minor bugfixes
Add installation options for PETSc and SLEPc
Add iterative solver for absorption proabilities
Fix docstring issues
Fix installation by including future-fstrings.
Initial beta pre-release.