Skip to main content

Within-Sample Normalization

Normalize expression values within each sample.

Default variant: clip-Q3__log1p (Q3 clipping + log1p transform)

Methods​

Background Correction​

  • Quantile-based clipping (Q3, Q5)
  • Centering

Variance Stabilization​

  • asinh transform (cofactor 5 or 10)
  • log1p transform

Default Variant​

clip-Q3__log1p: Q3 quantile clipping + log1p transform

CLI​

celltype-refinery preprocess normalize \
  --input filtered/ \
  --method clip-Q3__log1p \
  --out output/normalized