| name | marker_gene_validator |
| description | Validate whether a marker set supports a proposed cell type or cell state and explain the main caveats. |
| category | bio/single_cell_rna |
| version | 1 |
| requires_tools | ["search_knowledge_base","ncbi_eutils","uniprot_api","python_repl"] |
| requires_network | true |
| user_invocable | true |
| tags | ["markers","validation","annotation","cell-state"] |
| aliases | ["marker_panel_validator"] |
| species | any |
| modality | single_cell_rna |
| stage | annotation |
| stability | stable |
| safety_level | low |
Marker Gene Validator
Purpose
Check whether a proposed marker set really supports the claimed cell identity or state.
When to use
Use this skill when the user already has a marker panel or top DE genes and wants to know whether the label is convincing.
Required inputs
- markers: a list of marker genes
- proposed label: cell type or state
- context (optional): species, tissue, disease, stimulation, or assay context
Steps
- Restate the proposed label, species, tissue, and disease or stimulation context because the same markers can mean different things across systems.
- Search local guidance such as marker panel notes with
search_knowledge_base before leaning on generic marker heuristics.
- Use
ncbi_eutils and uniprot_api to confirm unclear, surprising, or multifunctional markers when necessary.
- Use
python_repl to organize markers into strongly supportive, weakly supportive, and conflicting groups if the list is long.
- Return a confidence judgment that clearly separates well-supported markers from context-dependent or contradictory ones.
Output format
- Biological context or assumptions: proposed label, species, tissue, and any inferred activation or disease context.
- Evidence or source basis: which
search_knowledge_base, ncbi_eutils, uniprot_api, and python_repl checks support the call.
- Marker assessment: supportive markers, conflicting markers, and confidence in the proposed label.
- Caveats or ambiguity: lineage overlap, activation-state confounding, or insufficient marker coverage.
- Recommended next step: what marker, modality, or follow-up validation would most reduce uncertainty.
Failure modes
- Too few markers: say confidence is limited.
- Conflicting markers: return alternative labels or mixed-state possibilities.
- Broad label: ask for more context if the claim is underspecified.
Examples
- "Do PDCD1, TOX, TIGIT, LAG3 support an exhausted CD8 T-cell label?"
- "Are these markers enough to call this cluster macrophages?"
