scirpy.datasets.wu2020_3k¶
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scirpy.datasets.wu2020_3k()¶ Return the dataset from [WMdA+20] as AnnData object, downsampled to 3000 TCR-containing cells.
This is how the dataset was processed:
import scanpy as sc import pandas as pd # Use this list of 3k barcodes for consistency with previous versions barcodes = pd.read_csv("./3k_barcodes.csv", header=None)[0].values adata = sc.read_h5ad("wu2020.h5ad") adata = adata[barcodes, :].copy() adata.write_h5ad("wu2020_3k.h5ad", compression="lzf")