dandelion.preprocessing.external.recipe_scanpy_qc

dandelion.preprocessing.external.recipe_scanpy_qc(self, max_genes=2500, min_genes=200, mito_cutoff=5, pval_cutoff=0.1, min_counts=None, max_counts=None, blacklist=None)[source]

Recipe for running a standard scanpy QC workflow.

Parameters
  • adata (AnnData) – annotated data matrix of shape n_obs × n_vars. Rows correspond to cells and columns to genes.

  • max_genes (int) – naximum number of genes expressed required for a cell to pass filtering. Default is 2500.

  • min_genes (int) – minimum number of genes expressed required for a cell to pass filtering. Default is 200.

  • mito_cutoff (float) – maximum percentage mitochondrial content allowed for a cell to pass filtering. Default is 5.

  • pval_cutoff (float) – maximum Benjamini-Hochberg corrected p value from doublet detection protocol allowed for a cell to pass filtering. Default is 0.05.

  • min_counts (int, optional) – minimum number of counts required for a cell to pass filtering. Default is None.

  • max_counts (int, optional) – maximum number of counts required for a cell to pass filtering. Default is None.

  • blacklist (sequence, optional) – if provided, will exclude these genes from highly variable genes list.

Returns

Return type

AnnData of shape n_obs × n_vars where obs now contain filtering information. Rows correspond to cells and columns to genes.