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bulk-rnaseq-gsea-custom-db

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Streamline custom gene-set integration for GSEA.

Data & Analytics#id-mapping#gsea#gene-sets#master-table#rnaseq#clusterProfiler#homologene
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Automates the integration and processing of non-MSigDB gene-set databases for clusterProfiler GSEA, enabling standardized T2G/T2N conversion and master-table compatibility.

Core Features & Use Cases

  • Parse and normalize custom gene-set databases (GMX/TSV/CSV/igraph) into T2G/T2N.
  • Support cross-species ID mapping (homologene, AnnotationDbi) and gene symbol passthrough.
  • Quality control and deduplication (size filtering, Jaccard deduplication) and master-table normalization.

Quick Start

Provide a two-column TSV file and the tool will output GSEA-ready T2G and T2N objects and append results to the master table.

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

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