cellrank.datasets.reprogramming_schiebinger

cellrank.datasets.reprogramming_schiebinger(path='datasets/reprogramming_schiebinger.h5ad', subset_to_serum=False, **kwargs)[source]

Reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells from [Schiebinger et al., 2019].

sc-RNA-seq dataset comprising 236 285 cell recorded using 10X Chromium at 39 time points spanning days 0-18 past reprogramming initiation.

Contains total-counts normalized, log-transformed counts and low-dimensional embedding coordinates (force-directed). Moreover, it contains the following obs annotations:

  • 'day' - time-point information.

  • 'serum'/'2i' - whether this cell comes from the serum/2i condition.

  • 'cell_sets' - cluster labels.

Parameters:

  • path (str | Path) – Path where to save the dataset.

  • subset_to_serum (bool) – Whether to return the full object or subsetted to the serum condition. This subset also contains the pre-computed transition matrix.

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

Return type:

AnnData

Returns:

: Annotated data object.

Notes

The full dataset has approximately 1.4GiB.