ID: biomedical.genomics.cell_annotation
Version: 1.1.0
Status: Integrated & Downloaded
Category: Genomics / Single-Cell Annotation
CellTypeAgent is an LLM-driven framework for automated cell type annotation in scRNA-seq data. It interprets marker genes, assigns labels, and generates explanations with confidence scores.
| Field | Type | Notes |
|---|---|---|
markers |
list[str] | Marker genes per cluster |
species |
str | human or mouse |
tissue |
str | Optional tissue context |
reference |
str | Optional atlas reference |
- Cell type labels per cluster
- Confidence score and evidence markers
- Suggested ambiguous or mixed identities
cd repo
pip install -r requirements.txt
python repo/main.py --data your_data.h5ad- Do not over-specify cell types without marker support.
- Use tissue context to resolve ambiguous marker sets.
- Flag clusters with mixed signatures for manual review.