tomas.lrt.extract_DE

tomas.lrt.extract_DE(adata, pval_cutoff=0.05, logFC_cutoff=0)

Extract DE results from Anndata into a table.

Parameters:

  • adata (AnnData) – The (annotated) UMI count matrix of shape n_obs × n_vars. Rows correspond to droplets and columns to genes.

  • pval_cutoff (float, optional) – Significance level. The default is 0.05.

  • logFC_cutoff (float, optional) – Cutoff of log2-foldchange to tell the DE significance. The default is 0.

Returns:

DE_all – Organize DE results into a tabel.

Return type:

pandas.DataFrame