Clean Genes and Cells with Metacell2

Usage

clean_genes_and_cells(
  anndata,
  properly_sampled_min_cell_total = 800,
  properly_sampled_max_cell_total = 8000,
  properly_sampled_max_excluded_genes_fraction = 0.1,
  exclude_genes = "",
  exclude_gene_patterns = "",
  seed = 123456
)

Arguments

anndata: anndata object containing Single Cell Expression Data
properly_sampled_min_cell_total: exclude all cells with UMI count below this threshold
properly_sampled_max_cell_total: exclude all cells with UMI count above this threshold
properly_sampled_max_excluded_genes_fraction: exclude all cells whose sum of excluded data divided by the toal is more then the threshold
exclude_genes: gene names to exlude
exclude_gene_patterns: gene patterns to exclude
seed: seed for reproducibilty