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bulk-rnaseq-gsea

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End-to-end bulk RNA-seq GSEA pipeline with MSigDB and custom databases.

Data & Analytics#visualization#pathway-analysis#gsea#master-table#msigdb#bulk-rnaseq#custom-databases
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Bulk RNA-seq GSEA analysis unifies enrichment testing and downstream visualization by connecting limma-voom DE results to MSigDB and non-MSigDB gene-set databases, and by assembling a single master table for cross-database comparisons.

Core Features & Use Cases

  • Executes MSigDB GSEA via clusterProfiler/fgsea with idempotent checkpointing
  • Integrates custom gene-set databases (MitoPathways, mitoXplorer, TransportDB, GATOM) and normalizes results to a common schema
  • Produces a unified 13-column master_gsea_table.csv suitable for Python visualization and interactive dashboards
  • Provides a complete pipeline from DE ranking to pathway-level visualization and pathway-explorer-ready outputs

Quick Start

Run the bulk-rnaseq-gsea workflow on your DE results to generate MSigDB and custom-gene-set GSEA checkpoints and export the master_gsea_table.csv for visualization.

Dependency Matrix

Required Modules

None required

Components

scriptsreferences

💻 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
Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#bulk-rnaseq-gsea

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