Merge pull request #106 from mcvickerlab/dev

Jaureguy760 · web-flow · commit c0df8e1dfe98 · 2026-04-19T02:43:31.000-07:00
chore: promote dev → master (comparative_imbalance removed)
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -71,7 +71,6 @@ Documentation
 
    tutorials/bulk_workflow
    tutorials/single_cell_workflow
-   tutorials/comparative_imbalance
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/source/tutorials/bulk_workflow.rst b/docs/source/tutorials/bulk_workflow.rst
@@ -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
diff --git a/docs/source/tutorials/comparative_imbalance.rst b/docs/source/tutorials/comparative_imbalance.rst
diff --git a/docs/source/tutorials/single_cell_workflow.rst b/docs/source/tutorials/single_cell_workflow.rst
@@ -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
 ------------------------
@@ -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
diff --git a/docs/source/user_guide/analysis.rst b/docs/source/user_guide/analysis.rst
@@ -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
 -----
@@ -92,4 +94,3 @@ Next Steps
 ----------
 
 * :doc:`counting` to generate bulk or single-cell counts
-* :doc:`/tutorials/comparative_imbalance` for group-comparison workflows
diff --git a/docs/source/user_guide/single_cell.rst b/docs/source/user_guide/single_cell.rst
@@ -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
