AD pathway-enrichment
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results.
As a process D 49/100 · Unfinished process — weak spots: result and completion, inputs and preconditions, failures and branches
How to improve
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 0
✓ No critical or high findings
Files scanned: 5. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
✓ No remarks against the Agent Skills spec
Process rating: all ten parameters 49/100
- 0Result and completion. Does not say what the result is
- 0Inputs and preconditions. Does not say what the process needs to start
- 0Failures and branches. Linear process with no failure handling
- 30Running it twice. 3 mutating operations with no state check
- 60Tools and files. Uses tools (bash, web, python) that frontmatter does not declare
- 70When it triggers. States when to use, but not when not to
- 85Steps. 26 steps, 1 vague phrases
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 3098 tokens
- 100Progress reporting. Reports progress
- low 12 top-level sections: this looks like several domains in one skill
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +4Description does not say when NOT to use the skill (false activations)
- +3Description length 1010: 120–800 characters recommended
- +3Output format is not stated: the model decides each time
- +2Single-language instructions
- +5Description quotes 7 example trigger phrases
- +4Structure: 23 headings
- +3Step-by-step instructions: 26 items
- +4Has examples (5 code blocks)
- +4Reference files are cited in the instructions (3 of 3)
- +3All 1 scripts are documented
- +1License stated
Quality base 70; lint remarks subtract, signals add up to 100. Result: 94.