cellrank.datasets.pancreas_preprocessed

cellrank.datasets.pancreas_preprocessed(path='datasets/endocrinogenesis_day15.5_preprocessed.h5ad', **kwargs)

Development of the murine pancreas at E15.5 from [Panc19], preprocessed according to the basic tutorial.

Parameters

• path (Union[str, Path]) – Path where to save the dataset.

• **kwargs – Keyword arguments for scanpy.read().

Returns

adata – Annotated data object.

Return type

anndata.AnnData

Examples

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

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

Fit models and plot gene trends

Kernel tricks