cellrank.datasets.reprogramming_morris#
- cellrank.datasets.reprogramming_morris(subset=ReprogrammingSubset.FULL, path='datasets/reprogramming_morris.h5ad', **kwargs)[source]#
Reprogramming of mouse embryonic fibroblasts to induced endoderm progenitors at 8 time points from [Biddy et al., 2018].
sc-RNA-seq dataset comprising 104 887 cell recorded using 10X Chromium and Drop-seq [Macosko et al., 2015] at 8 time points spanning days 0-28 past reprogramming initiation.
Contains raw spliced and unspliced count data, low-dimensional embedding coordinates as well as clonal information from CellTagging [Biddy et al., 2018]. Moreover, it contains the following
anndata.AnnData.obs
annotations:‘reprogramming_day’ - time-point information.
‘reprogramming’ - whether this clone is enriched for cells from successfully reprogrammed populations.
‘CellTagDN_XXk’ - CellTag from day N from the XXk cells
subset
.
- Parameters:
subset (
Literal
['full'
,'48k'
,'85k'
]) –Whether to return the full object or just a subset. Can be one of:
’full’ - return the complete dataset containing 104 887 cells.
’85k’ - return the subset as described in [Biddy et al., 2018] Fig. 1, containing 85 010 cells.
’48k’ - return the subset as described in [Biddy et al., 2018] Fig. 3, containing 48 515 cells.
kwargs (
Any
) – Keyword arguments forscanpy.read()
.
- Return type:
- Returns:
: Annotated data object.
Notes
The dataset has approximately 1.5GiB and the subsetting is performed locally after the full download.