single-cell-annotation-skills-with-omicverse
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-annotation --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 annotation skills with omicverse ## Overview Use this skill to reproduce and adapt the single-cell annotation playbook captured in omicverse tutorials: SCSA [`t_cellanno.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_cellanno.ipynb), MetaTiME [`t_metatime.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_metatime.ipynb), CellVote [`t_cellvote.md`](../../../omicverse_guide/docs/Tutorials-single/t_cellvote.md) & [`t_cellvote_pbmc3k.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_cellvote_pbmc3k.ipynb), CellMatch [`t_cellmatch.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_cellmatch.ipynb), GPTAnno [`t_gptanno.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_gptanno.ipynb), and label transfer [`t_anno_trans.ipynb`](../../../omicverse_guide/docs/Tutorials-single/t_anno_trans.ipynb). Each section below highlights required inputs, training/inference steps, and how to read the outputs. ## Instructions 1. **SCSA automated cluster annotation** - *Data requirements*: PBMC3k raw counts from 10x Genomics (`pbmc3k_filtered_gene_bc_matrices.tar.gz`) or the processed `sample/rna.h5ad`. Download instructions are embedded in the notebook; un
- Overview
- Instructions
- Critical API Reference - EXACT Function Signatures
- pySCSA - IMPORTANT: Parameter is clustertype, NOT cluster
- COSG Marker Genes - Results stored in adata.uns, NOT adata.obs
- Common Pitfalls to Avoid
- Examples
- References
What does the single-cell-annotation-skills-with-omicverse skill do?
Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill single-annotation --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.