Menü
Advise on doublet detection and removal for scRNA (scrublet, scDblFinder, best practices).
Mit Codex oder Claude installieren Kopieren Sie diesen Prompt, fügen Sie ihn in Codex, Claude oder einen anderen Assistant ein und lassen Sie die Skill-Seite prüfen und installieren.
Basierend auf der SOC-Berufsklassifikation
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 | doublet_detection_advice |
| description | Advise on doublet detection and removal for scRNA (scrublet, scDblFinder, best practices). |
| category | bio/single_cell_rna |
| version | 1 |
| requires_tools | ["search_knowledge_base"] |
| requires_network | false |
| user_invocable | true |
| species | any |
| modality | single_cell_rna |
| stage | qc |
| stability | experimental |
| safety_level | low |
User asks about doublets in single-cell data: how to detect, which tool, or when to remove.
Local: Use search_knowledge_base for lab SOPs on doublet detection.
Summarize: Explain that doublets are two cells in one droplet; recommend tools (Scrublet for 10x, scDblFinder for flexibility). Mention expected rate (~0.4% per 1k cells for 10x).
Workflow: Suggest: run doublet scoring → set threshold or use automatic → filter or label. Note not to over-filter.
Caveats: Brief note on multiplet rate vs sequencing depth.
