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Triage whether ambient RNA contamination is a plausible explanation for suspicious single-cell expression patterns.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.
| name | ambient_rna_triage |
| description | Triage whether ambient RNA contamination is a plausible explanation for suspicious single-cell expression patterns. |
| category | bio/single_cell_rna |
| version | 1 |
| requires_tools | ["search_knowledge_base","python_repl"] |
| requires_network | false |
| user_invocable | true |
| tags | ["ambient-rna","soup","contamination","triage"] |
| aliases | ["ambient_contamination_check"] |
| species | any |
| modality | single_cell_rna |
| stage | qc |
| stability | stable |
| safety_level | low |
Assess whether ambient RNA contamination is a likely contributor to unexpected marker expression or noisy cluster interpretation.
Use this skill when the user reports improbable marker expression, broad low-level contamination, or suspicious signals in droplet-based single-cell data.
knowledge/ambient-rna-troubleshooting.md with search_knowledge_base.python_repl only if you need to organize a checklist or risk table.