القائمة
Run or interpret gene set enrichment (Enrichr/g:Profiler) and summarize results.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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 | gene_set_enrichment |
| description | Run or interpret gene set enrichment (Enrichr/g:Profiler) and summarize results. |
| category | bio/single_cell_rna |
| version | 1 |
| requires_tools | ["fetch_url","python_repl"] |
| requires_network | true |
| user_invocable | true |
| species | any |
| modality | single_cell_rna |
| stage | interpretation |
| stability | experimental |
| safety_level | low |
User has a list of genes (e.g. DE genes) and wants enrichment against GO, KEGG, Reactome, or similar.
Normalize: Parse gene list into a clean list (max ~500 for API limits).
Enrichr: Use Enrichr API if available:
https://maayanlab.cloud/Enrichr/addList then GET results from https://maayanlab.cloud/Enrichr/enrich with ontology (e.g. GO_Biological_Process_2021, KEGG_2021_Human).Or g:Profiler: fetch_url to g:Profiler API with gene list and sources (GO, KEGG, REAC).
Parse: Extract top 10–15 terms: term name, p-value, adjusted p-value, genes overlapping.
Interpret: One paragraph summary: what biological processes/pathways are enriched and what that suggests.