cellrank.datasets.reprogramming_schiebinger

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

Reprogramming of mouse embryonic fibroblasts to induced pluripotent stem cells at 39 time points from [Schiebinger et al., 2019].

scRNA-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 anndata.AnnData.obs annotations:

‘day’ - time-point information.

‘serum’/’2i’ - whether this cell comes from the serum/2i condition.

‘cell_sets’ - cluster labels.

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.

Notes

The dataset has approximately 1.4GiB.