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Suggest Scanpy/Python commands for basic scRNA QC (filtering, mito, UMI).
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 | scanpy_qc_commands |
| description | Suggest Scanpy/Python commands for basic scRNA QC (filtering, mito, UMI). |
| category | bio/single_cell_rna |
| version | 1 |
| requires_tools | ["python_repl"] |
| requires_network | false |
| user_invocable | true |
| species | any |
| modality | single_cell_rna |
| stage | qc |
| stability | experimental |
| safety_level | low |
User wants ready-to-run Scanpy (or AnnData) code for QC: calculate_QC_metrics, filter cells/genes, normalize.
Default thresholds: If not given, use common defaults (e.g. mito < 20%, min_genes 200, min_cells 2).
Code: Use python_repl or output a code block with:
Present: Copy-pastable code and one-line note on adjusting thresholds.
