Rank genes by differential expression to identify enriched pathways in single-cell data.
npx skills add https://github.com/pwwang/immunopipe --skill scfgsea
Please help me install this Agent Skill. Skill: scfgsea Source: https://github.com/pwwang/immunopipe/tree/main/skills/scfgsea Command: npx skills add https://github.com/pwwang/immunopipe --skill scfgsea
Quickly identifying enriched biological pathways in single-cell datasets by analyzing ranked genes derived from differential expression, enabling interpretable pathway-level insights.
Run scfgsea on a ranked gene list derived from Seurat clusters to identify enriched pathways.
High-intent search queries and answers about installing and using this skill.
You can perform GSEA on single-cell RNA-seq data by ranking genes using differential expression between cell groups and computing enrichment scores, p-values, and NES with the fgsea R package.
The best way to identify enriched pathways in Seurat clusters is to run fgsea-powered GSEA on a ranked gene list derived from cluster differential expression to generate enrichment scores and publication-ready plots.
Yes, you can use custom GMT gene sets for single-cell pathway analysis. The tool applies configurable gene sets to ranked gene lists to identify enriched pathways across cluster comparisons and subgroup studies.
To rank genes for GSEA in disease vs control single-cell studies, calculate differential expression between the conditions and use the resulting ranked gene list as input to compute enrichment scores and p-values.
Outputs from fgsea analysis of single-cell data include enrichment scores, p-values, normalized enrichment scores (NES), and publication-ready visualizations that are exportable for downstream reporting.
tassiovaleAnalyze gene lists or ranked data for enriched biological pathways and gene sets.
dailycafiMap metabolites to KEGG, Reactome, and SMPDB pathways with enrichment and topology analysis.
pwwangRank metabolic pathways across scRNA-seq groups using GSEA-based enrichment.
jaechang-hitsPerform GSEA and ORA on gene lists with Enrichr pathway lookups.
