Find biological pathways in gene lists
pathway-enrichmentskillsetup L2★27,559
K-Dense-AI/scientific-agent-skills ↗What it does
Run ORA or GSEA to identify enriched biological pathways in gene lists
Best for
Interpreting DE genes, CRISPR hits, or cluster markers into biological pathways
Inputs
- · gene list or ranked gene scores
- · gene-set library (GO, KEGG, MSigDB)
Outputs
- · enrichment table
- · p-values, FDR, NES scores
- · dotplot visualization
Requires
- · gseapy
- · g:Profiler
- · Enrichr
- · MSigDB
- · KEGG
Preconditions
Gene symbols are valid; background universe chosen
Failure modes
Wrong method chosen (ORA vs GSEA); gene-ID mapping failed; multiple-testing correction ignored
Trust signals
- · ORA/GSEA decision tree provided
- · background universe guidance
- · setup/install instructions precise