ehrapy.preprocessing.sqrt_norm(adata, vars=None, copy=False)[source]#

Apply square root normalization.

Take the square root of all values.

  • adata (AnnData) – AnnData object containing X to normalize values in. Must already be encoded using encode().

  • vars (str | Sequence[str] | None) – List of the names of the numeric variables to normalize. If None all numeric variables will be normalized. Defaults to None .

  • copy (bool) – Whether to return a copy or act in place. Defaults to False .

Return type:

AnnData | None


AnnData object with normalized X. Also stores a record of applied normalizations as a dictionary in adata.uns[“normalization”].


>>> import ehrapy as ep
>>> adata = ep.dt.mimic_2(encoded=True)
>>> adata_norm = ep.pp.sqrt_norm(adata, copy=True)