genomics

Identify differential gene expression patterns from RNA-seq and transcriptomics data.

44|13|Updated Nov 15, 2025
One-click install
npx skills add https://github.com/openscientist-io/openscientist --skill genomics-openscientist-io
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: genomics
Source: https://github.com/openscientist-io/openscientist/tree/main/skills/domain/genomics
Command: npx skills add https://github.com/openscientist-io/openscientist --skill genomics-openscientist-io

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Genomics and transcriptomics analyses are complex and time-consuming; this skill provides a structured approach to design, execute, and interpret differential expression studies and pathway enrichment to derive mechanistic insights from genomics data.

Core Features & Use Cases

  • Differential Expression Guidance: Plan and perform differential expression analyses for RNA-seq and microarray data, including normalization and multiple-testing correction.
  • Pathway & Gene Set Interpretation: Map results to GO, KEGG, and other pathways to identify affected biological processes.
  • Best Practices & Nomenclature: Apply gene symbol conventions and robust reporting for reproducible results.
  • End-to-End Workflows: Provide templates that combine transcriptional data with basic integrative analyses for hypothesis generation.

Quick Start

Provide an end-to-end genomics analysis plan for an RNA-seq dataset, returning differential expression results and pathway insights.

Frequently Asked Questions about genomics

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

FAQPage Schema
How do I analyze differential gene expression from RNA-seq data?

Differential gene expression analysis from RNA-seq data requires structured normalization and multiple-testing correction to identify significant patterns. This workflow applies robust statistical testing to bulk and single-cell transcriptomics datasets to generate clear, actionable summaries.

What is the best way to perform pathway enrichment on transcriptomics results?

Pathway enrichment on transcriptomics results maps differential expression outputs to GO and KEGG databases to identify affected biological processes. This gene-set interpretation step translates lists of significant genes into mechanistic insights for hypothesis generation.

Can I use this workflow for both bulk and single-cell expression analyses?

Yes, this workflow supports both bulk and single-cell expression analyses for identifying differential gene expression patterns. It applies consistent normalization and multiple-testing correction across both data types to ensure reproducible results.

How do I interpret GO and KEGG mappings for gene-set analysis?

Interpreting GO and KEGG mappings for gene-set analysis involves matching differentially expressed genes to known biological pathways and processes. This approach identifies affected molecular mechanisms and provides clear summaries suitable for generating research hypotheses.

Do I need to normalize RNA-seq data before differential testing?

Yes, normalization is required before differential testing to ensure accurate identification of differential gene expression patterns. The workflow applies normalization and multiple-testing correction to RNA-seq and transcriptomics data to produce robust, reproducible results.