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chore: promote dev → master (comparative_imbalance removed) #106

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Merged
Jaureguy760 merged 1 commit into from
Apr 19, 2026
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chore: promote dev → master (comparative_imbalance removed) #106

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1 change: 0 additions & 1 deletion docs/source/index.rst
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Expand Up @@ -71,7 +71,6 @@ Documentation

tutorials/bulk_workflow
tutorials/single_cell_workflow
tutorials/comparative_imbalance

.. toctree::
:maxdepth: 2
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1 change: 0 additions & 1 deletion docs/source/tutorials/bulk_workflow.rst
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Expand Up @@ -170,4 +170,3 @@ See Also
- :doc:`/methods/mapping_filter` — canonical WASP filter contract
- :doc:`/methods/statistical_models` — the LRT and beta-binomial model
- :doc:`/tutorials/single_cell_workflow` — single-cell RNA-seq / ATAC-seq
- :doc:`/tutorials/comparative_imbalance` — comparing groups
188 changes: 0 additions & 188 deletions docs/source/tutorials/comparative_imbalance.rst
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5 changes: 2 additions & 3 deletions docs/source/tutorials/single_cell_workflow.rst
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Expand Up @@ -75,8 +75,8 @@ Step 3 — Compare groups (optional)
--phased \
--out_file differential_imbalance.tsv

For multi-group and all-pairs comparisons, visualization, and
interpretation, see :doc:`comparative_imbalance`.
Omit ``--groups`` to compare all available groups pairwise. See
:doc:`/user_guide/analysis` for the full CLI reference and output columns.

Per-cell vs. pseudo-bulk
------------------------
Expand Down Expand Up @@ -162,4 +162,3 @@ See Also
- :doc:`/user_guide/analysis` — analysis CLI reference
- :doc:`/methods/statistical_models` — beta-binomial LRT
- :doc:`bulk_workflow` — sibling tutorial for bulk RNA-seq / ATAC-seq
- :doc:`comparative_imbalance` — comparing groups
5 changes: 3 additions & 2 deletions docs/source/user_guide/analysis.rst
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Expand Up @@ -66,7 +66,9 @@ Comparative Single-Cell Analysis
--out_file compare_ai.tsv

This compares allelic imbalance between the requested groups and writes one TSV
per comparison.
per comparison. Each output has per-group columns ``mu1`` and ``mu2`` alongside
the pooled-null ``combined_mu``, plus ``null_ll`` / ``alt_ll`` / ``pval`` /
``fdr_pval``.

Notes
-----
Expand All @@ -92,4 +94,3 @@ Next Steps
----------

* :doc:`counting` to generate bulk or single-cell counts
* :doc:`/tutorials/comparative_imbalance` for group-comparison workflows
1 change: 0 additions & 1 deletion docs/source/user_guide/single_cell.rst
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Expand Up @@ -373,7 +373,6 @@ the specified groups, using a likelihood ratio test with FDR correction.

For comprehensive coverage of comparative analysis, see:

* :doc:`/tutorials/comparative_imbalance` - Detailed comparative analysis tutorial
* :doc:`analysis` - Statistical methods for comparative imbalance

See Also
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