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bulk-rnaseq-gsea-msigdb

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Speed MSigDB GSEA on bulk RNA-seq with caching.

Data & Analytics#pathway-analysis#gsea#fgsea#clusterProfiler#msigdb#bulk-rnaseq#limma-voom
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

What problem does it solve?

MSigDB GSEA analysis on pre-ranked RNA-seq differential expression results, enabling robust pathway enrichment with clusterProfiler/fgsea while managing MSigDB loading, API compatibility, and checkpoint caching.

Core Features & Use Cases

  • Run GSEA against MSigDB collections (Hallmark, C2, C3, C5) using the RNAseq-toolkit wrapper.
  • Load MSigDB gene sets via msigdbr with compatibility across v7.5 and v8+ APIs.
  • Benefit from checkpoint caching to speed up iterative analyses and support standalone run_gsea_analysis workflows.

Quick Start

Load your DE results, configure the MSigDB databases you want (H, C2, C3, or C5), and run the run_gsea() wrapper to perform a GSEA analysis against MSigDB collections.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: bulk-rnaseq-gsea-msigdb
Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#bulk-rnaseq-gsea-msigdb

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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