CellRank for directed single-cell fate mapping¶
CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules: kernels compute cell-cell transition probabilities and estimators generate hypothesis based on these. Our kernels work with a variety of input data including RNA velocity [La Manno et al., 2018] and [Bergen et al., 2020], cellular similarity (both transcriptomic and spatial) and pseudotime, among others. Our VelocityKernel takes into account uncertainty in the velocities and allows you to aggregate the short-range fate relations given by RNA velocity into longer trends along the phenotypic manifold. Our main estimator is Generalized Perron Cluster Cluster Analysis (G-PCCA) [Reuter et al., 2018] which coarse-grains the Markov chain into a set of macrostates which represent initial, terminal and intermediate states. For each transient cell, we compute its fate probability towards any terminal state. We show an example of such a fate map in the figure above, which has been computed using the data of [Bastidas-Ponce et al., 2019]. CellRank combines kernels and estimators with a powerful plotting API, enabling you to visualize e.g. smooth gene expression trends along lineages or fate-informed circular embeddings, to name just a few.
Getting started with CellRank¶
If you’re new to CellRank, make sure to go though the basic tutorial which introduces you to CellRank’s high-level API. Most biological systems require a bit more control, so be sure to check out the kernels and estimators tutorial which allows to unlock the full power of CellRank. If you want to see individual functions in action, visit our gallery.
This release includes:
cellrank.tl.estimators.GPCCA.plot_macrostate_composition()to visualize macrostate composition over a categorical variable PR 641.
cellrank.tl.estimators.BaseEstimator.plot_lineage_drivers_correlation()to plot lineage driver correlation with 2 lineages in a scatter plot PR 640.
Dramatically speed-up the computation of fate probabilities (>5x) PR 638.
Remove 4 technical examples and add 2 new examples PR 602:
Prune requirements.txt PR 571.
Fix not checking whether probabilities sum to 1 in
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.
CellRank’s key applications¶
compute initial & terminal as well as intermediate macrostates of your biological system
infer fate probabilities towards the terminal states for each individual cell
visualize gene expression trends along specific lineages while accounting for the continuous nature of fate determination
identify potential driver genes for each identified cellular trajectory
Why is it called “CellRank”?¶
CellRank does not rank cells, we gave the package this name because just like Google’s original PageRank algorithm, it works with Markov chains to aggregate relationships between individual objects (cells vs. websites) to learn about more global properties of the underlying dynamics (initial & terminal states and fate probabilities vs. website relevance).
We actively encourage any contribution! To get started, please check out both the contribution guide as well as the external API. CellRank’s modular structure makes it easy to contribute, be it a new method to compute cell-cell transition probabilities (kernels), a new way to analyze a transition matrix (estimators) or an addition to the plotting API. If you’re thinking of contributing a new kernel, we have a kernel tutorial that guides you trough the process.