bio-pathway-wikipathways
PKU-YuanGroup/OpenAI4STests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and…
Scores out of 100 · grade A
2026-08-22Works
40% of the score92/100
- Frontmatter name `bio-pathway-wikipathways` does not match its directory `bio-pathway-analysis-wikipathways`.
Maintained
25% of the score100/100
- no commits in the last 12 weeks
Adopted
20% of the score35/100
- 335 stars on the source repo.
Documented
15% of the score90/100
- 2,211 words with worked examples.
- Ships 3 bundled files.
Install
npx skills add PKU-YuanGroup/OpenAI4S/bio-pathway-wikipathwaysWhat the check found
| Finding | What it means |
|---|---|
| Name mismatch | The frontmatter name and the directory name disagree. |
What it says it does
Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways. Covers why a WikiPathways result is a snapshot of a live, monthly-updated database (enrichWP/gseWP/gson_WP silently pull data.wikipathways.org/current/), why reproducibility requires pinning a dated GMT via downloadPathwayArchive(date=, format='gmt'), why the WP GMT is Entrez-keyed so symbols and Ensembl silently overlap nothing, why universe=NULL gives a biased all-WP-genes background, how to split the name%version%wpid%org term, and why WikiPathways (CC0, no peer review) complements KEGG/Reactome. Use when running open community-pathway enrichment, covering a non-model WP species, catching disease/drug pathways missing from KEGG/Reactome, or needing a reproducible dated analysis. The gene list comes from differential-expression/de-results; visualize with enrichment-visualization.
Also in PKU-YuanGroup/OpenAI4S
| Artifact | Score | What the check found | Type | Reach | Last commit |
|---|---|---|---|---|---|
| bio-atac-seq-allele-specific-accessibilityPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-atac-peak-callingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-consensus-peaksetPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-deep-learning-atacPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-atac-seq-footprintingPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today | |
| bio-causal-genomics-effector-gene-prioritizationPKU-YuanGroup/OpenAI4S | clean | Skill | 335 stars | today |
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