single-cell-downstream-analysis
Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-downstream-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Single-cell downstream analysis quick-reference This skill sheet distills the OmicVerse single-cell downstream tutorials into an executable checklist. Each module highlights **prerequisites**, the **core API entry points**, **interpretation checkpoints**, **resource planning notes**, and any **optional validation or export steps** surfaced in the notebooks. ## AUCell pathway scoring (`t_aucell.ipynb`) - **Prerequisites** - Download pathway collections (GO, KEGG, or custom) that match the organism under study before running the tutorial. - Ensure an `AnnData` object with clustering/embedding (`adata.obsm['X_umap']`) is prepared. - **Core calls** - `ov.single.geneset_aucell` for one pathway; `ov.single.pathway_aucell` for multiple pathways. - `ov.single.pathway_aucell_enrichment` to score all pathways in a library (set `num_workers` for parallelism). - **Result checks** - Interpret AUCell scores as expression-like values (0–1). Use `sc.pl.embedding` to confirm pathway activity patterns. - Run `sc.tl.rank_genes_groups` on the AUCell `AnnData` to find cluster-enriched pathways and visualize with `sc.pl.rank_genes_groups_dotplot`. - **Resources** - Library-wide scoring can be CPU-inte
- AUCell pathway scoring (taucell.ipynb)
- scRNA-seq DEG (bulk-style meta cell) (tscdeg.ipynb)
- scRNA-seq DEG (cell-type & composition) (tdegsingle.ipynb)
- scDrug response prediction (tscdrug.ipynb)
- SCENIC regulon discovery (tscenic.ipynb)
- cNMF program discovery (tcnmf.ipynb)
- NOCD overlapping communities (tnocd.ipynb)
- Lazy pipeline & reporting (tlazy.ipynb)
What does the single-cell-downstream-analysis skill do?
Checklist-style reference for OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-downstream-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.