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Resolve "DEG/DAR Notebook"

Stefan Nitz requested to merge 241-deg-dar-notebook into dev

Closes #241 (closed)

Part I

  • Replace tools.marker_genes.run_deseq2 with a pure python implementation
    • Update Code
    • Update Dependencies
    • UpdateTests
  • Reduce lines of code in rna_analysis/notebooks/0A_marker_gene.ipynb -> Looked at it with @hendrik.schultheis, Nothing to do
  • move the notebook to general_notebooks, add to CI
  • make sure it also works with atac data
  • check notebook formatting guidelines
  • add changes to CHANGES.rst

Part II

  • Rework the marker_genes notebook The notebook should find marker genes and score them with scanpy and pydeseq2 and recommend a choice. The user should then be able to choose.
Edited by Stefan Nitz

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