scanpy.datasets.ebi_expression_atlas

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

Load a dataset from the EBI Single Cell Expression Atlas.

The atlas can be browsed online to find the accession you want. 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 E-GEOD-98816.

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

Returns:

Annotated data matrix.

Example

>>> import scanpy as sc
>>> sc.datasets.ebi_expression_atlas("E-MTAB-4888")  
AnnData object with n_obs × n_vars = 2261 × 23899
    obs: 'Sample Characteristic[organism]', 'Sample Characteristic Ontology Term[organism]', ..., 'Factor Value[cell type]', 'Factor Value Ontology Term[cell type]'