cospar.datasets.reprogramming

cospar.datasets.reprogramming(data_des='CellTagging')

The reprogramming dataset from

• Biddy, B. A. et al. Single-cell mapping of lineage and identity in direct reprogramming. Nature 564, 219–224 (2018).

This dataset has multiple time points for both the clones and the state measurements. The cells are barcoded over 3 rounds during the entire differentiation process. There are multiple ways to assemble the barcodes on day 0, day 3, and day 13 into a clonal ID. Below, we provide three variants:

• Concatenate barcodes on day 0 and day 13, as in the original analysis (adata.obsm[‘X_clone_Concat_D0D3’], the default);

• Concatenate barcodes on day 0, day 3, and day 13 (adata.obsm[‘X_clone_Concat_D0D3D13’]);

• No concatenation; each cell has up to 3 barcodes (adata.obsm[‘X_clone_NonConcat_D0D3D13’]).

The last choice keeps the nested clonal structure in the data. You can choose any one of the clonal arrangement for downstream analysis, by setting adata_orig.obsm[‘X_clone’]=adata_orig.obsm[‘X_clone_Concat_D0D3’]. The three clonal arrangements give very similar fate prediction.

Parameters

data_des : str

A key to label this dataset.