scib.preprocessing.hvg_intersect

scib.preprocessing.hvg_intersect(adata, batch, target_genes=2000, flavor='cell_ranger', n_bins=20, adataOut=False, n_stop=8000, min_genes=500, step_size=1000)

Highly variable gene selection

Legacy approach to HVG selection only using HVG intersections between all batches

Parameters:

  • adata – anndata object with preprocessed counts

  • batch – adata.obs column

  • target_genes – maximum number of genes (intersection reduces the number of genes)

  • min_genes – minimum number of intersection HVGs targeted

  • step_size – step size to increase HVG selection per dataset

Returns:

list of maximal target_genes number of highly variable genes