moscot.datasets.tedsim

moscot.datasets.tedsim(path='~/.cache/moscot/tedsim.h5ad', force_download=False, **kwargs)

Dataset simulated with TedSim [Pan et al., 2022].

Simulated scRNA-seq dataset of a differentiation trajectory. For each cell, the dataset includes a (raw counts) gene expression vector as well as a lineage barcodes. The data was simulated with asymmetric division rate of \(0.2\), intermediate state step size of \(0.2\) and contains the following fields:

• obsm['barcodes'] - barcodes.

• obsp['cost_matrices'] - precomputed lineage cost matrices.

• uns['tree'] - lineage tree in the Newick format.

• uns['couplings' ] - coupling matrix based on the ground-truth lineage tree.

Parameters:

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

• force_download (bool) – Whether to force-download the data.

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

Return type:

AnnData

Returns:

: Annotated data object.