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🎨 rename enrichment group to upregulated in x - #82

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enryH wants to merge 8 commits into
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updt_enrichment_analysis
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🎨 rename enrichment group to upregulated in x#82
enryH wants to merge 8 commits into
mainfrom
updt_enrichment_analysis

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@enryH

@enryH enryH commented Jul 20, 2026

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Summary

Upregulated vs Downregulated can be confusing. Therefore we switch to upregulated in group 1 vs upregulated in group 2.

Related to Multiomics-Analytics-Group/vuecore#45

...

List of changes proposed in this PR (pull-request)

  • direction column entries are changed to reflect upregulated in x

Checks

In case you add a new module or update one, please check the following tasks:

  • The folder names defines the name of the subpackage (module)
  • Add the user-facing functions to the __init__.py in the new folder, so that
    they are available when the subpackage is imported.
  • Create Pandera schema in a file with subpackage name in the src/acore/types folder.
    Optimal is to have only one output schema of results per subpackage or module.
  • Add a relatively small and public dataset to the data folder, or reuse an existing one for testing
  • Create an api example jupyter notebook in the docs/api_examples_module folder with that data
  • Use jupytext to sync the Jupyter notebook with a Python script
  • Update index.md file in the docs folder with the new example
  • Create test script in the /tests folder with the name of the subpackage or module
    using pytest or unittests to test your new functionality.

@enryH
enryH marked this pull request as ready for review August 6, 2026 07:19
@enryH
enryH requested a lite review from Copilot August 6, 2026 07:19

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Pull request overview

This PR updates enrichment analysis output labeling to avoid the potentially confusing “upregulated vs downregulated” terminology by switching to “upregulated in ” for both directions (group1 vs group2).

Changes:

  • Updated run_up_down_regulation_enrichment to emit direction as upregulated in {g1} / upregulated in {g2}.
  • Updated the expected direction values in the enrichment integration test to match the new labeling.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File Description
src/acore/enrichment_analysis/__init__.py Changes direction strings to “upregulated in {group}” for both branches.
tests/enrichment_analysis/test_enrichment.py Updates expected direction values to the new “upregulated in timepointX” labels.

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Comment thread src/acore/enrichment_analysis/__init__.py
Comment thread tests/enrichment_analysis/test_enrichment.py Outdated
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2 participants