Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.
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Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI