Description
pathway-enrichment is an agent skill for pathway and gene-set enrichment analysis, on gene lists or on ranked gene data, and for interpreting the results. It is the usual last step after a differential expression analysis, a screen or clustering. The skill explains the choice that matters most, between two methods. Over-representation analysis takes a thresholded gene list, such as genes with an adjusted p-value below 0.05, and tests whether it overlaps a gene set more than chance, using Fisher's exact or hypergeometric tests. Tools such as Enrichr and g:Profiler do this. Gene set enrichment analysis, GSEA, uses the whole ranked list with no threshold, and tests whether each gene set is concentrated towards the top or bottom of the ranking, which works better when effects are broad and subtle. Preranked GSEA uses a score per gene, such as the DESeq2 statistic. The skill covers the gene-set databases behind these analyses, including GO, KEGG, Reactome, WikiPathways and MSigDB Hallmark sets, and it covers scoring of gene sets per sample or per cell with ssGSEA or GSVA.…
Highlights
- Over-representation analysis on gene lists
- Preranked GSEA on ranked gene data
- GO, KEGG, Reactome, WikiPathways and Hallmark sets
- ssGSEA and GSVA scoring
- Guidance on background and gene IDs
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pathway-enrichment FAQ
What is the difference between ORA and GSEA?
ORA tests a thresholded gene list for overlap with gene sets. GSEA uses the whole ranked list and tests whether each set is concentrated at the top or bottom.
Which tools does it name?
Enrichr and g:Profiler for over-representation, and preranked GSEA for ranked data.
Which gene-set databases are covered?
GO, KEGG, Reactome, WikiPathways and MSigDB Hallmark sets, among others.
Can it score gene sets per sample?
Yes. It covers ssGSEA and GSVA for per-sample or per-cell scoring.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill pathway-enrichment.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best pathway-enrichment alternatives?
Popular alternatives to pathway-enrichment include cellxgene-census, gget and adaptyv. See all pathway-enrichment alternatives