scrna-cell-type-annotator

npx skills add majiayu000/claude-skill-registry --skill scrna-cell-type-annotator --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# ScRNA Cell Type Annotator Automatically annotate cell clusters from scRNA-seq data using marker gene signatures, tissue context, and species-specific references. ## Input Validation This skill accepts: per-cluster marker gene lists from scRNA-seq experiments, with tissue type and species context, for automated cell type annotation. If the request does not involve scRNA-seq cluster annotation — for example, asking to perform bulk RNA-seq DEG analysis, run clustering from raw counts, or interpret proteomics data — do not proceed. Instead respond: > "scrna-cell-type-annotator is designed to annotate cell clusters from single-cell RNA data using marker genes. Your request appears to be outside this scope. Please provide cluster marker lists with tissue and species context, or use a more appropriate tool for your task. For clustering from raw counts, use Seurat or Scanpy preprocessing pipelines." ## When to Use - Post-clustering annotation of Seurat/Scanpy clusters - Novel cell type discovery in unexplored tissues - Cross-study comparison of cell type compositions - Cell atlas construction and harmonization ## Quick Check ```bash python -m py_compile scripts/main.py python scripts/mai

python -m py_compile scripts/main.py
python scripts/main.py --help
python scripts/main.py --demo
pip install -r requirements.txt