sc_toolbox.tools.generate_pseudobulk#

sc_toolbox.tools.generate_pseudobulk(adata, group_key='identifier', sep='\\t', save=None)[source]#

Generates a pseudobulk for a given key of groups in the AnnData object.

Looks like:

Genes

Group Member 1

Group Member 2

Gene 1

Value 1

Value 2

Gene 2

Value 2

Value 3
Parameters:

  • adata (AnnData) – AnnData object

  • group_key (str) – The key to group by. E.g. by mice, by condition, … (default: ‘identifier’)

  • sep – Separator to use when saving the pseudobulk table (default: ‘ ‘)

  • save (Optional[str]) – Path to save the pseudobulk table to (default: None)

Return type:

DataFrame

Returns:

A Pandas DataFrame containing the pseudobulk table