scib.preprocessing.hvg_batch

scib.preprocessing.hvg_batch(adata, batch_key=None, target_genes=2000, flavor='cell_ranger', n_bins=20, adataOut=False)

Batch-aware highly variable gene selection

Method to select HVGs based on mean dispersions of genes that are highly variable genes in all batches. Using a the top target_genes per batch by average normalize dispersion. If target genes still hasn’t been reached, then HVGs in all but one batches are used to fill up. This is continued until HVGs in a single batch are considered.

Parameters:

  • adata – anndata object

  • batch – adata.obs column

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

  • flavor – parameter for scanpy.pp.highly_variable_genes

  • n_bins – parameter for scanpy.pp.highly_variable_genes

  • adataOut – whether to return an anndata object or a list of highly variable genes