bio-single-cell-cell-annotation
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill cell-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.
## Version Compatibility Reference examples tested with: pandas 2.2+, scanpy 1.10+, scikit-learn 1.4+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Automated Cell Type Annotation ## CellTypist (Python) **Goal:** Automatically annotate cell types using a pre-trained or custom CellTypist model. **Approach:** Load a reference model, predict cell types with majority voting for cluster-level consensus, and add predictions to AnnData. **"Automatically label my cell types"** → Apply a trained classifier to assign cell type identities based on transcriptomic similarity to a reference atlas. ```python import celltypist import scanpy as sc adata = sc.read_h5ad('adata_processed.h5ad') # List available models celltypist.models.models_description() # Download model celltypist.models.download_models(model='Immune_All_Low.pkl') # Load model model = cell
- Version Compatibility
- CellTypist (Python)
- CellTypist with Custom Model
- SingleR (R)
- SingleR Fine Labels
- Azimuth (R/Seurat)
- scPred (R)
- Annotation Confidence Filtering
- Consensus Annotation
- Compare Annotations
- Marker-Based Validation
- Related Skills
What does the bio-single-cell-cell-annotation skill do?
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling. Use when automatically annotating cell types using reference datasets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cell-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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.