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QC rework

Hendrik Schultheis requested to merge qc_rework into dev

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:

qc notebook overview

Edited by Mette Bentsen

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