scellrun 1.3.4

Opinionated, report-first CLI for single-cell and multi-omics analysis. Sane defaults baked in, defensible deliverables out.

scellrun

A scRNA-seq CLI with a decision log so two analysts — or two LLM agents — on the same data give the same answer.

中文版 README

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Why this exists

Two analysts on the same scRNA dataset reanalyze it and the cluster count differs by ~20% (Lähnemann et al., 2020 / PMC9122178). The reason is rarely the science — it's the dozens of tiny choices nobody writes down: mt% ceiling, HVG count, integration method, clustering resolution, panel pick. Six months later nobody remembers which knob got tweaked.

scellrun is what you put on top of scanpy so every one of those choices ends up in a single grep-able file with a reason next to it. Same data → same defaults → same output, every time. If a reviewer asks "why mt% 20?" you read line 14 of 00_decisions.jsonl to them.

It's not a workflow manager (use nf-core for cluster orchestration), and it doesn't replace scanpy — it calls scanpy under the hood with opinionated parameters and an audit trail.

Quick start

conda create -n scellrun python=3.11 -y
conda activate scellrun
pip install scellrun

scellrun analyze data.h5ad --tissue "OA cartilage"
# → ./scellrun_out/run-<ts>/05_report/index.html

Got cellranger output instead of an .h5ad?

scellrun scrna convert path/to/cellranger_outs -o data.h5ad
scellrun analyze data.h5ad --tissue "OA cartilage"

Add --lang zh for a Chinese report. Add --profile joint-disease for cartilage / synovium / subchondral bone. Walkthrough in docs/quickstart.md.

What you actually get

• Five-stage one-shot: QC → integrate (Harmony) → markers → annotate → report. One command, one HTML you can email.
• Decision log at <run>/00_decisions.jsonl — every non-trivial choice with a one-sentence reason. Greppable; auto/user/ai source labels.
• Five tissue profiles — default, joint-disease (Fan 2024 chondrocyte panel), tumor, brain, kidney. One Python file each, contribute yours.
• Self-check — each stage detects pathologies (panel mismatch, all-fragmented clusters, single-sample-no-batch) and proposes the cheapest fix. --auto-fix applies it.
• Reviewer loop — scellrun review <run> runs a tiny local Flask app for cluster relabels, threshold tweaks, and notes; analyze --apply-overrides <json> re-runs with the human's edits as source="user" rows.
• PDF export — scellrun export <run> --format pdf for publication.

Who this is for

• The LLM agent (Claude Code, Hermes, Codex, OpenClaw) handling a clinician's request. This is the primary user. Drop skills/scellrun/SKILL.md into your agent's skill directory; the agent then knows which command maps to which user intent, how to read the decision log, when to surface a self-check trigger.
• The clinician-bioinformatics team that wants every project to look the same. Same QC layout, same decision table, same provenance trail across samples, students, rotations.
• The reviewer asking "why mt% 20?" Open 00_decisions.jsonl; the answer is on line 14, verbatim.

docs/agent-demo.md is a verbatim Claude Code transcript running scellrun end-to-end on real OA cartilage data, including the agent quoting the decision log when the user asks "why res=0.3?".

What the decision log looks like

{"stage":"qc","key":"max_pct_mt","value":20.0,"default":20.0,"source":"auto",
 "rationale":"mt% ceiling 20% — joint tissue is stress-prone, the textbook 10% silently drops real chondrocytes (PI cohort 2024-2026, AIO PM=20)"}
{"stage":"analyze","key":"method_downgrade","value":"none","default":"harmony","source":"auto",
 "rationale":"no sample/batch column in obs — single-sample input; auto-downgraded --method from harmony to none"}
{"stage":"analyze","key":"chosen_resolution_for_annotate","value":0.3,"source":"auto",
 "rationale":"fewest singletons → most balanced (every resolution fragmented) — picked res=0.3: n_clusters=13, largest=31.5%, smallest=0.2%, singletons=2"}
{"stage":"analyze","key":"annotate.auto_panel","value":"celltype_broad","source":"auto",
 "rationale":"swapped to celltype_broad: chondrocyte_hits=2, broad_hits=9; required >=1.5x margin to keep chondrocyte panel"}

source is auto (built-in heuristic), user (a CLI / review override), or ai (an LLM call). attempt_id groups rows by invocation; fix_payload carries the structured fix on self-check *.suggest rows. Full schema in skills/scellrun/SKILL.md.

v1.3.2 onwards the chosen_resolution_for_annotate rationale, panel auto-pick reasoning, and self-check triggers all surface in the HTML report's "At a glance" section so a reader doesn't have to grep the jsonl to learn why a particular resolution / panel got picked.

Profiles

A profile is community-encoded working practice for a tissue domain — defaults + marker panels in one Python file.

profile	mt%	hb%	panels	notes
default	20%	—	—	fresh-tissue 10x v3 baseline (OARSI ceiling)
joint-disease	20%	tight	Fan 2024 11-subtype chondrocyte + 15-group broad	cold-validated; auto-swaps to broad on immune-rich data
tumor	20%	—	TISCH/Sun 2021 pan-cancer TME (broad only)	not yet cold-validated
brain	10%	—	Tasic/Hodge cortical-hippocampal (broad only)	not yet cold-validated
kidney	15%	—	KPMP/Stewart 2019 nephron + immune (broad only)	not yet cold-validated

scellrun profiles list
scellrun profiles show joint-disease   # thresholds + panels

Tissue or disease working practice diverging from the defaults? Contribute a profile — one Python file under src/scellrun/profiles/. See docs/contributing.md.

Status

v1.3 frozen surface — scRNA only. v1.x is now in maintenance mode. Bug fixes and additive scRNA profiles only; no new public commands. Bulk RNA-seq, metabolomics, and proteomics extensions are deferred to a future v2.0; see ROADMAP.md.

CLI surface (qc / integrate / markers / annotate / analyze / review / export / profiles) is locked for the v1.x series.

Feature support matrix

Status legend: ✅ shipped · 🚧 planned (next minor) · 💤 deferred (no timeline) · ⏳ v2.0 scope

scRNA core

• ✅ QC: per-cell metrics (mt% / ribo% / hb% / n_genes / doublets), flag-don't-drop policy
• ✅ Multi-sample merge (anndata.concat) + cell-cycle scoring (Tirosh)
• ✅ PCA → Harmony integration + multi-resolution sweep with quality scoring
• ✅ Wilcoxon marker DE (logfc ≥ 1, pct ≥ 0.25, positive-only)
• ✅ Panel auto-pick annotation + LLM second opinion (--ai) + PubMed evidence (--pubmed)
• ✅ Decision log (00_decisions.jsonl) + self-check (SC* triggers) + --auto-fix retry
• ✅ HTML report (05_report/index.html) + views layer (06_views/) + PDF export (scellrun[export])
• ✅ Reviewer loop (scellrun review) → analyze --apply-overrides <json>

Normalization

• ✅ LogNormalize + scale (default)
• ✅ SCT-style Pearson residuals via scanpy.experimental.pp.normalize_pearson_residuals (--normalize sct)
• 💤 decontX ambient-RNA removal — no stable Python port; revisit when celda matures

Integration methods

• ✅ Harmony (default; auto-degrades to none on single-sample input)
• 🚧 RPCA / CCA — currently no-op + report note; scanpy ports unstable
• ⏳ scVI — probabilistic batch correction, parked for v2.0 multi-modal track

Tissue profiles (scellrun profiles list)

• ✅ default (fresh-tissue 10x v3 baseline)
• ✅ joint-disease (Fan 2024 11-subtype chondrocyte panel; cold-validated)
• ✅ tumor (TISCH 2.0 / Sun 2021 pan-cancer TME, broad only)
• ✅ brain (Tasic 2018 / Hodge 2019 cortical-hippocampal, broad only)
• ✅ kidney (KPMP / Stewart 2019 nephron + immune, broad only)
• 🚧 synovium fine-subtype split (currently bundled inside joint-disease)
• 🚧 tumor / brain / kidney fine-subtype panels (pending cold-validation)

Reporting and i18n

• ✅ English + Chinese HTML report templates (--lang en|zh)
• ✅ At-a-glance rationale rendering for resolution / panel auto-pick / self-check triggers
• ✅ Three-tier provenance trail in report (data / inference / literature)

Distribution

• ✅ PyPI (pip install scellrun)
• ✅ ClawHub agent-skill bundle
• ✅ Dockerfile in repo (one-stage conda + pip image)
• 🚧 conda-forge feedstock
• 🚧 Tagged Docker push to ghcr.io/drstrangerujn/scellrun

Multi-omics (v2.0)

• ⏳ Bulk RNA-seq (scellrun bulk *)
• ⏳ Metabolomics composite scoring
• ⏳ Proteomics integration
• ⏳ Modality-aware Profile schema + new template trees

Distribution

• PyPI: pip install scellrun (pypi.org/project/scellrun)
• ClawHub: clawhub install scellrun for agent skills (clawhub.ai/skills/scellrun)
• Docker: docker pull ghcr.io/drstrangerujn/scellrun:latest (v1.0+)

License

MIT — see LICENSE.

Acknowledgements

Defaults trace back to the Shi Lab in-house R AIO pipeline and clinician-bioinformatics working practice for OARSI / musculoskeletal research. The Fan 2024 chondrocyte panel ships under the joint-disease profile.