scib.preprocessing.normalize

scib.preprocessing.normalize(adata, min_mean=0.1, log=True, precluster=True, cluster_method='louvain', sparsify=True)

Normalise counts using the scran normalisation method

Using computeSumFactors function from scran package.

Parameters:

• adata – anndata object

• sparsify – whether to convert the count matrix into a sparse matrix

• precluster – whether to perform preliminary clustering for differentiated normalisation

• min_mean – parameter of scran’s computeSumFactors function

• log – whether to performing log1p-transformation after normalisation