tacco.utils.preprocess_single_cell_data

preprocess_single_cell_data(adata, hvg=True, scale=True, pca=True, inplace=False, min_cells=10, min_genes=10, verbose=1)[source]

Preprocess single cell data in a standardized way from bare counts as input.

Parameters:

  • adata – The AnnData to process

  • hvg – Whether the dat should be subset to highly variable genes

  • scale – Whether the data should be scaled

  • pca – Whether the pcas should be calculated

  • inplace – Whether the input AnnData instance should be changed to contain the processed data

  • min_cells – The minimum number of cells a gene must have to be not filtered out

  • min_genes – The minimum number of genes a cell must have to be not filtered out

  • verbose – Level of verbosity, with 0 (no output), 1 (some output), …

Returns:

The processed AnnData