scanpy.datasets.ebi_expression_atlas

scanpy.datasets.ebi_expression_atlas(accession, *, filter_boring=False)

Load a dataset from the EBI Single Cell Expression Atlas

Downloaded datasets are saved in the directory specified by datasetdir.

Parameters:

accession str

Dataset accession. Like E-GEOD-98816 or E-MTAB-4888. This can be found in the url on the datasets page, for example https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-98816/results/tsne.

filter_boring bool (default: False)

Whether boring labels in .obs should be automatically removed, such as labels with a single or n_obs distinct values.

Return type:

AnnData

Example

>>> import scanpy as sc
>>> adata = sc.datasets.ebi_expression_atlas("E-MTAB-4888")