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bio-de-results

Extract, filter, annotate, and export DESeq2 and edgeR differential expression results.

Updated Mar 30, 2026
Search Tags:#bioinformatics#differential-expression#data-export#deseq2#gene-annotation#edger
One-click install
npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-de-results
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-de-results
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/bio-differential-expression-de-results
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill bio-de-results

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

DE analysis of RNA-seq data often yields raw results that require cleaning, enrichment with gene annotations, and formatting for reporting. This skill consolidates extraction, filtering, annotation, and export into ready-to-share tables and reports.

Core Features & Use Cases

  • Extract & filter: Retrieve DE results from DESeq2 or edgeR and apply significance and effect-size thresholds.
  • Annotate: Enrich results with gene symbols, descriptions, and cross-database identifiers.
  • Export: Generate CSV or Excel workbooks with all results, significant subsets, and ranked lists for pathway analysis.
  • Use Case: A researcher finishes a differential expression analysis and needs publication-ready tables and a GSEA-ready gene list.

Quick Start

Run the workflow to extract DE results from a fitted DESeq2/edgeR model, annotate genes, and export ready-for-share reports.

Frequently Asked Questions about bio-de-results

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

FAQPage Schema
How do I filter DESeq2 results by padj and log2FoldChange for publication?▼

Annotate differential expression results by enriching them with gene symbols, descriptions, and cross-database identifiers, enabling cross-method comparison and preparing data for pathway analysis.

Can I export RNA-seq differential expression results to CSV and Excel?▼

Export differential expression results to CSV or Excel workbooks containing all results, significant subsets, and ranked lists, producing publication-ready reports and GSEA-ready gene lists for downstream analysis.

Does this workflow support extracting results from both DESeq2 and edgeR?▼

Extract differential expression results from both DESeq2 and edgeR fitted models, applying filters and enabling optional cross-method comparison to consolidate outputs from either RNA-seq analysis framework.

What is the best way to prepare GSEA-ready gene lists from RNA-seq analysis?▼

Prepare GSEA-ready gene lists by extracting and ranking differential expression results from DESeq2 or edgeR, applying baseMean and padj filters, then exporting the ranked subsets for pathway analysis.

How do I add gene annotations to edgeR differential expression output?▼

Add gene annotations to edgeR output by enriching the differential expression results with gene symbols, descriptions, and cross-database identifiers during the extraction and export workflow.

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