metalsinglecell.pp.highly_variable_genes

metalsinglecell.pp.highly_variable_genes(adata, n_top_genes=None, n_bins=20, flavor='seurat', min_mean=0.0125, max_mean=3.0, min_disp=0.5, max_disp=inf, layer=None, copy=False)

Highly variable genes (sc.pp.highly_variable_genes); writes adata.var columns.

n_top_genes=None (scanpy’s default) selects seurat/cell_ranger genes by the min_mean/max_mean/min_disp/max_disp cutoffs; an integer takes the top-N.

Parameters:

• n_bins (int)

• flavor (str)

• min_mean (float)

• max_mean (float)

• min_disp (float)

• max_disp (float)

• copy (bool)