Run GSEA, ORA, and decoupler enrichment on gene expression data.
npx skills add https://github.com/inflexa-ai/inflexa --skill enrichment-inflexa-ai
Please help me install this Agent Skill. Skill: enrichment Source: https://github.com/inflexa-ai/inflexa/tree/main/skills/enrichment Command: npx skills add https://github.com/inflexa-ai/inflexa --skill enrichment-inflexa-ai
This skill addresses the complexity of interpreting high-throughput omics data by providing a standardized, reproducible framework for functional enrichment and pathway activity inference.
Use the enrichment skill to perform a preranked GSEA on the provided DESeq2 results using the MSigDB hallmark gene sets.
High-intent search queries and answers about installing and using this skill.
Gene set enrichment analysis is performed using GSEA or ORA to identify biological pathways from differentially expressed genes. The skill guides database selection, like MSigDB Hallmark, and applies Benjamini-Hochberg FDR correction.
Pathway activity inference from single-cell profiles is supported using decoupler methods. The skill executes pathway activity inference alongside ssGSEA and GSVA to interpret single-cell gene expression data.
To avoid network-dependent KEGG calls during functional annotation, the skill enforces offline reference database resolution and methodological rigor, ensuring proper background selection for ORA and signed ranking for GSEA.
The enrichment skill supports GSVA and ssGSEA for pathway analysis, alongside GSEA, ORA, and decoupler-based activity inference. These methods provide comprehensive functional enrichment for high-throughput omics data.
Offline reference database resolution for GSEA is needed to ensure reproducible functional enrichment without network dependencies. The skill satisfies this requirement by resolving reference databases locally.
ORA requires proper background selection in functional enrichment to ensure statistically valid results. The skill enforces this methodological rigor alongside gene set size filtering and Benjamini-Hochberg FDR correction.
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