Rank metabolic pathways across scRNA-seq groups using GSEA-based enrichment.
npx skills add https://github.com/pwwang/immunopipe --skill metabolicfeatures
Please help me install this Agent Skill. Skill: metabolicfeatures Source: https://github.com/pwwang/immunopipe/tree/main/skills/metabolicfeatures Command: npx skills add https://github.com/pwwang/immunopipe --skill metabolicfeatures
Enrichment analysis helps researchers identify which metabolic pathways are active across different cell groups, enabling biological interpretation and hypothesis generation.
Run MetabolicFeatures on a Seurat object to generate pathway enrichment results and visualizations for each cluster.
High-intent search queries and answers about installing and using this skill.
To run metabolic pathway enrichment, provide a Seurat object with normalized data and a GMT file of metabolic gene sets. The analysis uses GSEA-based ranking via the fgsea algorithm to return NES, p-values, FDR, and summary plots for each cluster.
GSEA-based ranking identifies which metabolic pathways are active across different scRNA-seq cell groups. It uses the fgsea algorithm to generate NES, p-values, FDR, and visualizations, enabling biological interpretation and hypothesis generation.
Yes, a GMT file of metabolic gene sets is required along with a Seurat object containing normalized data. You must also configure group_by, prerank_method, and fgsea_args to execute the fgsea algorithm and generate enrichment results.
Yes, the analysis generates summary plots and GSEA enrichment curves to facilitate interpretation. These visualizations map enriched metabolic pathways across different scRNA-seq clusters, treatments, or cell states.
Configure group-level metabolic enrichment by setting the group_by parameter to target scRNA-seq treatments or states. This integrates with ScrnaMetabolicLandscape and MetabolicInput to produce cluster- or condition-specific enrichment results.
pwwangCompute NES scores for metabolic pathways across scRNA-seq cell groups.
ya-wayAnalyzes Reactome pathway enrichment for gene lists using enrichPathway and gsePathway.
ya-wayAnalyze metabolite-mediated cell-cell communication from scRNA-seq data.
Teng-bioPerform gene enrichment and pathway analysis with gseapy, PANTHER, STRING, and Reactome.
