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 [Bastidas-Ponce et al., 2019], preprocessed according to the basic tutorial.

Parameters

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

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

Return type

AnnData

Returns

adata : anndata.AnnData Annotated data object.

Examples

Plot projection

Plot random walks

Kernel tricks

Compute macrostates

Compute coarse-grained transition matrix

Compute terminal states using GPCCA

Compute absorption probabilities

Compute potential lineage drivers

Plot initial states

Plot terminal states

Plot lineages

Plot potential lineage drivers

Plot directed PAGA

Plot circular embedding

Plot gene trends

Plot a heatmap of expression trends

Plot cluster lineage

Plot aggregated cellular fates

Plot graph structures

Fit models and plot gene trends