skills.rest
tony-zhelonkin
tony-zhelonkinCOMMUNITY
Explore all skills by this author →
𝕏@TonyZhelonkinGitHub

annotate-te-rnaseq-data

Annotate Ensembl IDs to gene symbols and parse TE identifiers from featureCounts outputs.

1|Updated Nov 20, 2025
Search Tags:#ensembl#rnaseq#featurecounts#bulk-rnaseq#transposable-elements#biomart#dgelist
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill annotate-te-rnaseq-data
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: annotate-te-rnaseq-data
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/annotate-te-rnaseq-data
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill annotate-te-rnaseq-data

SYSTEM DOCUMENTATION & REQUIREMENTS

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.

Frequently Asked Questions about annotate-te-rnaseq-data

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I annotate Ensembl IDs to gene symbols for bulk RNA-seq counts?▼

Annotate Ensembl IDs to gene symbols for bulk RNA-seq counts by mapping identifiers via biomaRt and appending gene biotype metadata directly to the featureCounts output matrix for downstream analysis.

How do I parse transposable element identifiers for RNA-seq differential expression analysis?▼

Parse transposable element identifiers for RNA-seq analysis by splitting TE IDs into subfamily, family, and class components, enabling TE-aware differential expression workflows.

Can I build a combined gene and TE count matrix for edgeR or limma?▼

You can build a combined gene and TE count matrix that constructs edgeR DGEList objects, directly supporting downstream differential expression analysis in both edgeR and limma workflows.

Do I need R and Bioconductor packages to annotate RNA-seq count matrices?▼

Yes, you need R with Bioconductor packages and TE annotation utilities from the TE-RNAseq-toolkit to annotate RNA-seq count matrices and construct DGEList objects.

What's the best way to prepare featureCounts output for TE-aware differential expression?▼

Prepare featureCounts output for TE-aware differential expression by combining gene and TE counts into unified annotated matrices, then constructing DGEList objects for edgeR and limma analysis.

Related Skills

Explore More Data & Analytics Skills→
StarlitnightlyStarlitnightly
32

fastq-analysis-pipeline

Orchestrate RNA-seq analysis from FASTQ files to gene count matrices.

Community
Advanced
MubasherMohammedMubasherMohammed

de-summary

Summarize differential expression results from DESeq2, edgeR, or limma outputs.

Community
Intermediate
StarlitnightlyStarlitnightly
1.2k

Bulk RNA-seq differential expression with omicverse

Perform bulk RNA-seq differential expression analysis with omicverse.

Community
Intermediate
jaechang-hitsjaechang-hits
298

deseq2-differential-expression

Perform differential gene expression analysis on bulk RNA-seq count data with DESeq2.

Community
Advanced