Examples

This section contains various code snippets that demonstrate cellrank’s usage.

Estimators

Below is a gallery of examples for cellrank.tl.estimators.GPCCA and cellrank.tl.estimators.CFLARE.

Compute eigendecomposition

Compute Schur vectors

Compute Schur matrix

Compute macrostates

Compute coarse-grained transition matrix

Compute terminal states using GPCCA

Compute absorption probabilities

Compute potential lineage drivers

Fit estimator

Plotting

Below are examples for cellrank.pl plotting module.

Plot initial states

Plot terminal states

Plot lineages

Plot potential lineage drivers

Plot directed PAGA

Plot gene trends

Plot a heatmap of expression trends

Plot cluster lineage

Plot aggregated cellular fates

Plot graph structures

Plot circular embedding

Others

Below are examples not covered in other examples such as cellrank.tl.Lineage or cellrank.ul.models.BaseModel.

Fit models and plot gene trends

Lineage tricks

Kernel tricks