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annotate-te-rnaseq-data

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Annotates RNA-seq counts and TE IDs for analysis.

Data & Analytics#ensembl#rnaseq#featurecounts#bulk-rnaseq#transposable-elements#biomart#dgelist
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Annotates bulk RNA-seq count matrices with gene symbols (via Ensembl/biomaRt) and parses transposable element identifiers into subfamily, family, and class, then combines gene and TE counts into unified matrices for downstream differential expression analysis.

Core Features & Use Cases

  • Annotates Ensembl IDs to gene symbols and adds gene biotype metadata
  • Parses TE identifiers into subfamily, family, and class to enable TE-aware analyses
  • Builds combined gene+TE matrices and constructs edgeR DGEList objects for downstream workflows (edgeR/limma)

Quick Start

Run the annotation template to generate annotated outputs and DGELists for edgeR/limma analysis.

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: annotate-te-rnaseq-data
Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#annotate-te-rnaseq-data

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