bio-pathway-go-enrichment
PKU-YuanGroup/OpenAI4SRuns Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1,…
Scores out of 100 · grade A
2026-08-22Works
40% of the score92/100
- Frontmatter name `bio-pathway-go-enrichment` does not match its directory `bio-pathway-analysis-go-enrichment`.
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
- 2,816 words with worked examples.
- Ships 3 bundled files.
Install
npx skills add PKU-YuanGroup/OpenAI4S/bio-pathway-go-enrichmentWhat the check found
| Finding | What it means |
|---|---|
| Name mismatch | The frontmatter name and the directory name disagree. |
What it says it does
Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hypergeometric/Fisher 2x2 test phyper(k-1, M, N-M, n, lower.tail=FALSE). Covers why the BACKGROUND universe (not the gene list) is the null and decides significance, why omitting universe= is a bug, why enrichGO defaults to ont='MF' not 'BP', why pvalueCutoff filters p.adjust not raw p, why ORA discards effect magnitude and inherits GO-DAG true-path redundancy (simplify, topGO), why RNA-seq gene-length bias inflates long-gene terms (GOseq Wallenius), plus GeneRatio/BgRatio, bitr ID mapping, minGSSize/maxGSSize, groupGO. Use when a pre-selected gene list (DE hits, co-expression module, screen, GWAS-mapped) needs GO annotation. For a ranked no-cutoff analysis see gsea; for other databases see kegg-pathways, reactome-pathways, wikipathways; DE source is differential-expression/de-results; plots in 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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