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docs(tutorials): Tier-D reduction — 6 getting-started pages to 3#101

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Jaureguy760 merged 3 commits intodevfrom
feat/docs-reduction-tier-d
Apr 19, 2026
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docs(tutorials): Tier-D reduction — 6 getting-started pages to 3#101
Jaureguy760 merged 3 commits intodevfrom
feat/docs-reduction-tier-d

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Summary

Follow-up to PR #99 (Tier-B). PI feedback was "still too much text" — this PR collapses the getting-started surface from 6 pages (848 lines) to 3 pages (~520 lines), a further 39% reduction on the tutorial section specifically.

Tutorial information architecture — before / after

Before (6 pages, 848 lines):

Page Lines Role
`quickstart.rst` (top-level) 66 "5-minute quickstart" — install + count + analyze
`tutorials/quickstart_counting.rst` 151 "Count in 5 minutes" worked example
`tutorials/bulk_workflow.rst` 175 Full bulk RNA + ATAC pipeline (shipped in PR #99)
`tutorials/scrna_seq.rst` 112 scRNA-seq workflow
`tutorials/scatac_workflow.rst` 156 scATAC-seq workflow
`tutorials/comparative_imbalance.rst` 188 Group comparisons

After (3 pages, ~520 lines):

Page Lines Role
`tutorials/bulk_workflow.rst` 175 Bulk RNA + ATAC pipeline (unchanged)
`tutorials/single_cell_workflow.rst` 165 NEW — scRNA + scATAC with data-type callouts
`tutorials/comparative_imbalance.rst` 188 Group comparisons (2 inbound refs updated)

Changes (3 commits)

  1. c5dec76 — Delete top-level `quickstart.rst` (66 lines). Duplicated bulk_workflow intro; sole toctree entry removed.
  2. 098496a — Delete `tutorials/quickstart_counting.rst` (151 lines). Redundant with bulk_workflow step 2.
  3. 7f623fe — Create `tutorials/single_cell_workflow.rst` merging scrna_seq + scatac_workflow. Data-type difference reduces to GTF (scRNA) vs BED (scATAC) in `--feature`. Per-cell-vs-pseudobulk table preserved from old scatac; barcode-suffix troubleshooting preserved from old scrna. 7 inbound `:doc:` references updated across index.rst, choosing_workflow.rst, bulk_workflow.rst, faq.rst, user_guide/single_cell.rst, and comparative_imbalance.rst.

Verification

  • `sphinx-build -q -b html` completes; Tier-D introduces zero new warnings (3 pre-existing duplicate-citation warnings for `Kumasaka2016` / `vandeGeijn2015` across methods/ pages shipped in PR docs: reduce text volume (~47%) + fix scientific correctness issues #99's Tier-B — already on origin/dev + master; out of scope here)
  • `grep` for all deleted-page names in docs/ returns zero matches
  • No Python changes → ruff/pytest/Rust tests are no-ops (but will run on CI)

Cumulative reduction (across Tier-B + Tier-D)

Tutorial section alone: 3,495 → 520 lines (−85%).

This 66-line page duplicated content now served by tutorials/bulk_workflow.rst
(install + count-variants + find-imbalance). Sole toctree entry removed from
index.rst. No other docs referenced it.

Part of Tier-D tutorial reduction: 6 getting-started pages → 3.
The 151-line quickstart was redundant with bulk_workflow.rst (which covers
the same count-variants invocation as part of its step 2). Having two
"5-minute" entry points confused the information architecture.

Self-reference at line 150 was the only inbound pointer; no other docs
referenced it.

Part of Tier-D tutorial reduction: 6 getting-started pages → 3.
…orkflow

Before: scrna_seq.rst (112) + scatac_workflow.rst (156) = 268 lines of
parallel-structure tutorials that differed only in --feature argument
(GTF for genes, BED for peaks).

After: single_cell_workflow.rst (~155) covers both modalities with
data-type callouts, same pattern as bulk_workflow.rst. Preserves both
code examples, the per-cell vs pseudo-bulk decision table from the old
scATAC tutorial, and the barcode-suffix troubleshooting from both.

Updated 7 inbound :doc: references across:
- index.rst (toctree: 2 entries → 1)
- choosing_workflow.rst (4 references)
- bulk_workflow.rst (2 references collapsed to 1)
- faq.rst (1 reference)
- user_guide/single_cell.rst (1 reference)
- comparative_imbalance.rst (1 reference)

Part of Tier-D tutorial reduction: 6 getting-started pages → 3.
@Jaureguy760 Jaureguy760 merged commit 01bdf24 into dev Apr 19, 2026
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@Jaureguy760 Jaureguy760 deleted the feat/docs-reduction-tier-d branch April 19, 2026 08:43
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