mcvickerlab · Jaureguy760 · Apr 19, 2026 · Apr 19, 2026 · Apr 19, 2026 · Apr 19, 2026
diff --git a/docs/source/choosing_workflow.rst b/docs/source/choosing_workflow.rst
@@ -22,11 +22,11 @@ WASP2 supports four major data types. Use this guide to find your workflow.
    * - **scRNA-seq (10x)**
      - Cell Ranger BAM + VCF + barcodes
      - Per-cell or per-cell-type ASE
-     - :doc:`tutorials/scrna_seq`
+     - :doc:`tutorials/single_cell_workflow`
    * - **scATAC-seq (10x)**
      - Fragments/BAM + VCF + barcodes
      - Single-cell allelic imbalance in ATAC peaks
-     - :doc:`tutorials/scatac_workflow`
+     - :doc:`tutorials/single_cell_workflow`
 
 Decision Flowchart
 ------------------
@@ -39,13 +39,13 @@ Decision Flowchart
 **Step 2: Bulk or single-cell RNA-seq?**
 
 * Bulk RNA-seq → :doc:`tutorials/bulk_workflow`
-* 10x Chromium scRNA-seq → :doc:`tutorials/scrna_seq`
+* 10x Chromium scRNA-seq → :doc:`tutorials/single_cell_workflow`
 * Other single-cell protocol → see :doc:`user_guide/single_cell`
 
 **Step 3: Bulk or single-cell ATAC-seq?**
 
 * Bulk ATAC-seq → :doc:`tutorials/bulk_workflow` (use BED peak file as ``--region``)
-* 10x scATAC-seq → :doc:`tutorials/scatac_workflow`
+* 10x scATAC-seq → :doc:`tutorials/single_cell_workflow`
 
 Do I Need to Run the WASP Remapping Step?
 ------------------------------------------

diff --git a/docs/source/faq.rst b/docs/source/faq.rst
@@ -102,7 +102,7 @@ Any aligner that produces CB-tagged BAMs will work (STARsolo, Alevin-fry, etc.).
 
 Run WASP2 on the full BAM to get per-cell allele counts, then use the output
 with your cell type annotations in Python (AnnData/Scanpy) to aggregate by
-cell type. See :doc:`tutorials/scrna_seq` for an example.
+cell type. See :doc:`tutorials/single_cell_workflow` for an example.
 
 Output and Results
 ------------------

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -53,7 +53,6 @@ Documentation
    :caption: Getting Started
 
    installation
-   quickstart
    choosing_workflow
    faq
 
@@ -70,10 +69,8 @@ Documentation
    :maxdepth: 2
    :caption: Tutorials
 
-   tutorials/quickstart_counting
    tutorials/bulk_workflow
-   tutorials/scrna_seq
-   tutorials/scatac_workflow
+   tutorials/single_cell_workflow
    tutorials/comparative_imbalance
 
 .. toctree::

diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
diff --git a/docs/source/tutorials/bulk_workflow.rst b/docs/source/tutorials/bulk_workflow.rst
@@ -170,6 +170,5 @@ See Also
 - :doc:`/user_guide/analysis` — analysis CLI reference
 - :doc:`/methods/mapping_filter` — canonical WASP filter contract
 - :doc:`/methods/statistical_models` — the LRT and beta-binomial model
-- :doc:`/tutorials/scatac_workflow` — single-cell ATAC-seq
-- :doc:`/tutorials/scrna_seq` — single-cell RNA-seq
+- :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
@@ -184,5 +184,5 @@ See Also
 
 - :doc:`/user_guide/analysis` — analysis-CLI reference and parameters
 - :doc:`/user_guide/single_cell` — input data formats, barcode exports
-- :doc:`/tutorials/scrna_seq` — basic single-cell workflow
+- :doc:`/tutorials/single_cell_workflow` — single-cell scRNA/scATAC workflow
 - :doc:`/methods/statistical_models` — the LRT underlying this test
diff --git a/docs/source/tutorials/quickstart_counting.rst b/docs/source/tutorials/quickstart_counting.rst