seuratmap2ref
Map query single-cell datasets to high-quality reference atlases using Seurat's reference mapping workflow. Performs label transfer, UMAP projection, and integration with reference annotations without modifying query expression data. Enables transfer learning from curated atlases like Azimuth PBMC or custom tissue-specific references.
npx skills add majiayu000/claude-skill-registry --skill seuratmap2ref --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.
# SeuratMap2Ref Process Configuration ## Purpose Map query single-cell datasets to high-quality reference atlases using Seurat's reference mapping workflow. Performs label transfer, UMAP projection, and integration with reference annotations without modifying query expression data. Enables transfer learning from curated atlases like Azimuth PBMC or custom tissue-specific references. ## When to Use - **Reference-based annotation**: Well-curated reference atlas available for your tissue/cell type - **Transfer learning**: Leverage existing annotations from large-scale atlases (Azimuth, HCA) - **UMAP projection**: Visualize query cells on reference UMAP structure - **Label transfer**: Propagate cell type labels, gene scores, metadata from reference ## Configuration Structure ### Process Enablement ```toml [SeuratMap2Ref] cache = true ``` ### Input Specification ```toml [SeuratMap2Ref.in] srtobj = ["SeuratClustering"] ``` ### Environment Variables ```toml [SeuratMap2Ref.envs] # REQUIRED ref = "/path/to/reference.rds" # Reference Seurat object (RDS/h5seurat) use = "celltype" # Reference metadata column to transfer ident = "seurat_clusters" # Name for transferred labels in query # NORMALI
- Purpose
- When to Use
- Configuration Structure
- Process Enablement
- Input Specification
- Environment Variables
- External References
- Seurat Functions
- Configuration Examples
- Minimal (Azimuth PBMC)
- Custom with Multi-Level Transfer
- Large Dataset with Splitting
- Common Patterns
- Pattern 1: Azimuth PBMC Reference
What does the seuratmap2ref skill do?
Map query single-cell datasets to high-quality reference atlases using Seurat's reference mapping workflow. Performs label transfer, UMAP projection, and integration with reference annotations without modifying query expression data. Enables transfer learning from curated atlases like Azimuth PBMC or custom tissue-specific references.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill seuratmap2ref --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 majiayu000/claude-skill-registry, a repository with 534 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.