Run directory: run-20260430-151851
none
chondrocyte_markers
0.3
— 13 clusters
Unassigned — 6 cluster(s)InfC — 3 cluster(s)preInfC — 1 cluster(s)27 decisions logged across 5 stage(s). Rows shaded amber were user overrides; ai tags an AI-driven choice.
| source | key | value | default | rationale |
|---|---|---|---|---|
| user | profile |
joint-disease |
default
|
profile 'joint-disease' chosen; profiles ship tissue-tuned thresholds (mt%, hb%) and marker panels. |
| auto | assay |
scrna |
— | fresh-tissue scRNA defaults; mt% ceiling 20% from PI cohort |
| auto | species |
human |
— | drives mt/ribo/hb gene-pattern matching (uppercased; same regex covers MT-CO1 and mt-Co1) |
| auto | max_pct_mt |
20.0 |
— | mt% ceiling 20.0% — joint tissue is stress-prone, the textbook 10% silently drops real chondrocytes (PI cohort 2024-2026, AIO PM=20) |
| auto | min_genes |
200 |
— | min n_genes 200 — Ilicic 2016 / Luecken & Theis 2019 droplet-vs-cell floor |
| auto | max_genes |
4000 |
— | max n_genes 4000 — multiplet upper cap on 10x v3 chemistry; raise via --max-genes for high-RNA cell types (megakaryocytes, hepatocytes) |
| auto | flag_doublets |
True |
— | scrublet on; report score distribution, never auto-drop (AIO leaves DF result attached) |
| auto | raw_counts_check |
looks_like_raw |
— | input matrix sampled (200 rows): integer-valued + max>1 = looks_like_raw; non-integer with small max = looks_like_normalized; otherwise unknown |
| auto | lang |
en |
— | report language; both EN and ZH templates kept in sync |
| source | key | value | default | rationale |
|---|---|---|---|---|
| auto | method |
none |
harmony
|
--method 'none' chosen explicitly |
| auto | sample_key |
none | — | no sample/batch column in obs — single-batch run |
| auto | n_pcs |
30 |
— | PCA components for neighbours/UMAP; 30 covers most tissue heterogeneity |
| auto | resolutions |
[0.1, 0.3, 0.5, 0.8, 1.0] |
— | Leiden multi-resolution sweep; 5 values (default short sweep) |
| auto | regress_cell_cycle |
False |
— | off by default; turn on with --regress-cell-cycle if cycling cells dominate |
| source | key | value | default | rationale |
|---|---|---|---|---|
| auto | resolutions |
[0.1, 0.3, 0.5, 0.8, 1.0] |
— | auto-detected from leiden_res_* columns in the integrated h5ad |
| auto | logfc_threshold |
1.0 |
— | |log2fc| >= 1.0 — Seurat in-house default; tightens to 1.0 to drop near-zero-effect markers |
| auto | pct_min |
0.25 |
— | min fraction expressing >= 0.25 — drops genes hit by dropout in the focal cluster |
| auto | only_positive |
True |
— | positive-only markers (cluster-up) — what FindAllMarkers ships by default |
| source | key | value | default | rationale |
|---|---|---|---|---|
| user | profile |
joint_disease |
default
|
profile selects which marker panels are available for matching |
| user | panel |
chondrocyte_markers |
— | --panel 'chondrocyte_markers' forced |
| auto | resolution |
0.3 |
— | matching against leiden_res_0.3 clusters; the orchestrator picks this from integrate's quality table when called via `scellrun analyze` |
| auto | use_ai |
False |
— | AI second-opinion off — deterministic panel match only |
| auto | use_pubmed |
False |
— | PubMed lookup off — turn on with --pubmed for the literature evidence column |
| user | tissue |
OA cartilage |
— | tissue context 'OA cartilage' drives PubMed scoping and AI prompt |
| source | key | value | default | rationale |
|---|---|---|---|---|
| auto | method_downgrade |
none |
harmony
|
no sample/batch column (orig.ident/sample/batch/donor) in obs — single-sample input; auto-downgraded --method from harmony to none. Pass --method harmony explicitly to force the original behavior. |
| auto | chosen_resolution_for_annotate |
0.3 |
— | fewest singletons → most balanced (every resolution fragmented) — picked res=0.3: n_clusters=13, largest=31.5%, smallest=0.2%, singletons=2 |
| auto | annotate.auto_panel |
chondrocyte_markers |
— | fine-subtype panel preferred (chondrocyte hits dominate or are tied) |
| # | command | ran at | key params |
|---|---|---|---|
| 1 | analyze:qc |
2026-04-30T15:20:32.649120+00:00 |
profile=joint-disease
species=human
thresholds={'species': 'human', 'min_genes': 200, 'max_genes': 4000, 'min_counts': 500, 'max_pct_mt': 20.0, 'max_pct_ribo': 50.0, 'max_pct_hb': 2.0, 'min_cells_per_gene': 3, 'flag_doublets': True}
force=False
lang=en
attempt_id=cae89793d0f9470a9c7f38894928f304
|
| 2 | analyze:integrate |
2026-04-30T15:20:52.573352+00:00 |
method=none
sample_key=None
n_pcs=30
resolutions=[0.1, 0.3, 0.5, 0.8, 1.0]
regress_cell_cycle=False
species=human
use_ai=False
tissue=OA cartilage
lang=en
attempt_id=cae89793d0f9470a9c7f38894928f304
|
| 3 | analyze:markers |
2026-04-30T15:23:51.773654+00:00 |
resolutions=[0.1, 0.3, 0.5, 0.8, 1.0]
logfc_threshold=1.0
pct_min=0.25
only_positive=True
top_n=10
lang=en
attempt_id=cae89793d0f9470a9c7f38894928f304
|
| 4 | analyze:annotate |
2026-04-30T15:24:49.548069+00:00 |
profile=joint-disease
panel_name=chondrocyte_markers
resolution=0.3
use_ai=False
use_pubmed=False
tissue=OA cartilage
lang=en
attempt_id=cae89793d0f9470a9c7f38894928f304
|
--pubmed is enabled at the annotate stage, top recent PubMed papers per marker.
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