Resolve "DEG/DAR Notebook"
Closes #241 (closed)
Part I
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Replace tools.marker_genes.run_deseq2 with a pure python implementation -
Update Code -
Update Dependencies -
UpdateTests
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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
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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