Thanks for making Scanpy! It works wonderfully, and is in general easy to use.
However, I am confused by the exact meaning of QC metrics as calculated by scanpy.pp.calculate_qc_metrics. As used in multiple tutorials this one outputs ‘n_genes_by_counts’. I am struggling to understand exactly what this value means.
I cannot see a further explanation in the documentation for this function, but the pmb3ck tutorial list this as:
- the number of genes expressed in the count matrix
But I can still not wrap my head around exactly what it means.