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updated atac notebooks and qc

Jan Detleffsen requested to merge add_ragi into dev

This merge request contains several ATAC-seq related changes:

  • RAGI clustering evaluation added to clustering.py
  • fld_scoring.py to disintegrate fld scoring from nucleosomal utils before removing it completely in the upcoming weeks.
  • reorganised the ATAC-Notebooks to be up to date with the existing sctoolbox

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