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Add jupyter notebook for pseudobulk_DEA, add support dataset, update … #127

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  1. Add jupyter notebook for pseudobulk_DEA (pulled from original notebook of decoupler pseudobulking tutorial, with updates)
  2. Replace icon with PyDeseq2 icon, update yaml in tutorial registry
  3. Add support dataset for id mapping (as we experienced pybiomart API instability during development)

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@canergen canergen closed this Nov 13, 2024
@canergen canergen reopened this Nov 13, 2024
@flying-sheep
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flying-sheep commented Nov 18, 2024

Hi! The data directory is .gitignored for a reason, namely that many tutorials use it to download data into.

So the .gitignore line /data/ has to stay. You could add an exception for your data file instead.

Also there are a few other problems indicated by the checks failing. Please fix.

  • docs:

    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510004: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb.rst:510011: WARNING: Non-consecutive header level increase; H2 to H4 [myst.header]
    checking consistency... …/docs/notebooks/tutorial_pseudobulk_DEA.ipynb: WARNING: document isn't included in any toctree

  • JSON schema:

    Schema validation errors were encountered.
    tutorial-registry/tutorials/decoupler-pseudobulk-de/meta.yaml::$.tags[0]: 'pseudo-bulk' is not one of ['data structures', 'differential expression', 'functional analysis', 'concatenation', 'preprocessing', 'cell-type annotation', 'quality control', 'visualization', 'multimodal', 'data integration', 'perturbation', 'compositional analysis', 'RNA velocity', 'pseudotime', 'interoperability']

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