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.