QC rework
I restructured the quality control process and all the underlying functions.
This should fix #10 (closed).
TODO:
-
utilities.load_anndata -
utilities.saving_anndata -
marker_genes.label_genes -
analyser.qcmetric_calculator -
qc_filter.set_def_cuts -> qc_filter.find_thresholds -
qc_filter.refining_cuts -> refine_thresholds -
qc_filter.anndata_filter -
plotting.qcf_ploting -> plotting.qc_violins -
adjust notebook 2 -
write tests -
add logging aka add to adata.uns["infoprocess"]
Notebook overview:
Edited by Mette Bentsen