normalize counts

Normalize gene expression counts by setting the count per cell to a desired value.

Parameters

target_sum: float The new gene counts will sum to this value.

exclude_high_expr: bool Exclude (very) highly expressed genes for the computation of the normalization factor (size factor) for each cell. A gene is considered highly expressed, if it has more than max_fraction of the total counts in at least one cell. The not-excluded genes will sum up to target_sum.

log_tranform: bool Logarithmize data after normalization.

max_fraction: float If exclude_highly_expressed=True, consider cells as highly expressed that have more counts than max_fraction of the original total counts in at least one cell.

Web view

Python equivalent

import scanpy as sc

sc.pp.normalize_total(adata, target_sum=1, exclude_highly_expressed=False, max_fraction=0.05)