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Agent skill

Differential Expression Analysis

by aipoch in aipoch/medical-research-skills

A skill your agent uses when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and…

MITAuto-check passedResearch & Science

Install Differential Expression Analysis

skills CLI
$ npx skills add aipoch/medical-research-skills --skill differential-expression-analysis -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills differential-expression-analysis --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'awesome-med-research-skills/Data Analysis/differential-expression-analysis' .claude/skills/differential-expression-analysis && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
differential-expression-analysis
GitHub stars
2k
Token cost
~1.5k tokens
SKILL.md length
485 words
Files
13 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

A skill your agent uses when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and…

  • Works in 4 steps: Validate Input → Run Differential Expression → Filter Results → …
  • Analyzing bulk RNA-seq
  • SKILL.md covers When to Read External Files, Usage, Arguments and Input Format, plus 7 more sections
  • Runs R scripts from its folder

What it does

Differential Expression Analysis is an agent skill from aipoch/medical-research-skills. Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 16 other files, including scripts and reference files (for example `eval_report_differential-expression-analysis_result.json`, `references/algorithm.md` and `references/cli-guide.md`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • Analyzing bulk RNA-seq
  • Microarray expression data to identify differentially expressed genes between two biological groups (case vs control)
  • With volcano plots and heatmap visualization

Example prompts

  • “/differential-expression-analysis”

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Validate Input
  2. Run Differential Expression
  3. Filter Results
  4. Generate Visualizations

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 6 files in scripts/ (R), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Differential Expression Analysis loads about 1.5k tokens when it runs, and up to ~3k if it reads all its reference files. Until then it costs about 76 tokens; SKILL.md has 485 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~76
When it runs · the whole SKILL.md, loaded when a task matches
~1.5k
With references · SKILL.md plus every file in references/, read only if the agent opens them
~3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 485 words, ~1,522 tokens.

Download SKILL.mdSave it as .claude/skills/differential-expression-analysis/SKILL.md (or your agent's skills folder). This skill also uses 12 other files; get the full folder from GitHub.
name
differential-expression-analysis
description
Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. NOT for:single-cell RNA-seq, methylation analysis, non-expression data.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

Differential Expression Analysis

When to Read External Files

SituationFile to ReadPurpose
Need algorithm detailsreferences/algorithm.mdStatistical methods, formulas, assumptions
Need to run analysisscripts/main.RExecute: Rscript scripts/main.R --input_file ... --group_file ...
Encounter errorsreferences/troubleshooting.mdCommon errors and solutions
Need CLI examplesreferences/cli-guide.mdDetailed CLI usage examples
Need test datatests/data/Sample input files for testing

Usage

bash
Rscript scripts/main.R \
  --input_file ./expression_matrix.csv \
  --group_file ./group_info.csv \
  --output_dir ./output/ \
  --diff_method limma \
  --p_threshold 0.05 \
  --logfc_threshold 0.1 \
  --seed 42

Arguments

ShortLongTypeDefaultDescription
-i--input_filecharacterrequiredExpression matrix file (genes as rows, samples as columns)
-g--group_filecharacterrequiredGroup information file (sample ID + group columns)
-o--output_dircharacter./output/Output directory
-m--diff_methodcharacterlimmaMethod: limma, deseq2, edger, t, wilcox
-n--norm_methodcharacterTMMNormalization for edgeR: TMM, RLE, upperquartile
-p--p_thresholdnumeric0.05P-value threshold
-f--logfc_thresholdnumeric0.1Log fold change threshold
-s--seedinteger42Random seed for reproducibility

Input Format

Expression Matrix (input_file)

Genes as rows, samples as columns, CSV format with gene ID in first column.

csv
"","GSM1442228","GSM1442229","GSM1442230"
"0610006L08Rik",3.438,3.237,3.265
"0610007P14Rik",6.734,7.017,6.807
Group File (group_file)

CSV with sample ID and group columns.

csv
"ID","group"
"GSM1442228","Control"
"GSM1442229","Control"
"GSM1442230","DIC"

Output Files

FileDescription
Diffanalysis.csvComplete DE results with gene_id, logFC, Pvalue, Padj
volcano_plot.pdfVolcano plot with significance thresholds
heatmap.pdfHeatmap of top upregulated/downregulated genes
session_info.txtR session and package version info
temp/rdegs.csvSignificant differentially expressed genes
temp/Diffanalysis_filtered.csvFull results with group annotations

Workflow

Step 1: Validate Input
  • Check file existence
  • Validate sample matching between expression matrix and group file
  • Verify at least 2 samples per group
Step 2: Run Differential Expression
  • Choose method: limma, DESeq2, edgeR, t-test, or Wilcoxon
  • Calculate logFC and p-values
  • Apply multiple testing correction (Benjamini-Hochberg)
Step 3: Filter Results
  • Filter by p-value and logFC thresholds
  • Classify genes as Up, Down, or Not significant
Step 4: Generate Visualizations
  • Volcano plot showing significance vs fold change
  • Heatmap of top differential genes

Methods

Show full SKILL.md (196 more words)Show less
limma

Linear models for microarray and RNA-seq with empirical Bayes moderation. Recommended for normalized expression data (FPKM, TPM).

DESeq2

Negative binomial GLM with variance stabilization. Recommended for raw count data.

edgeR

Empirical Bayes methods with TMM normalization. Supports robust dispersion estimation.

t-test / Wilcoxon

Simple pairwise statistical tests. t-test for parametric, Wilcoxon for non-parametric.

Examples

Basic Usage (limma)
bash
Rscript scripts/main.R \
  -i expression_matrix.csv \
  -g group_info.csv \
  -o ./output \
  -m limma
With DESeq2 for Count Data
bash
Rscript scripts/main.R \
  -i count_matrix.csv \
  -g group_info.csv \
  -o ./output \
  -m deseq2
Custom Thresholds
bash
Rscript scripts/main.R \
  -i expression_matrix.csv \
  -g group_info.csv \
  -o ./output \
  -p 0.01 \
  -f 0.5

Error Handling

Common Errors
ErrorCauseSolution
SKILL_FILE_NOT_FOUNDInput file doesn't existCheck file path
SKILL_SAMPLE_MISMATCHSample names don't matchVerify group file matches expression matrix columns
SKILL_INVALID_DATALess than 2 groups or samples per groupCheck group file
SKILL_FILTER_ERRORNo significant genes foundRelax thresholds or check data quality
SKILL_DEPENDENCY_MISSINGR package not installedInstall required packages

IF error persists, READ: references/troubleshooting.md

Testing

Test with Sample Data
bash
# Check help
Rscript scripts/main.R --help

# Run with sample data
Rscript scripts/main.R \
  -i tests/data/Combined_Datasets_Matrix_mus.csv \
  -g tests/data/Combined_Datasets_mus_Group.csv \
  -o tests/output/
Validation Commands
bash
# Count lines in output
wc -l output/Diffanalysis.csv

# Check volcano plot exists
ls -la output/volcano_plot.pdf

Implementation Checklist

  • CLI parsing with optparse
  • set.seed() for reproducibility
  • requireNamespace() dependency checks
  • Session info recording
  • Temp file cleanup
  • File reading instructions in SKILL.md
  • Modular script structure (<100 lines per file)
  • Test data provided
  • Error handling with SKILL_* codes
  • Scripts in scripts/ directory
  • References in references/ directory

Last updated: 2026-04-01 | Version: 2.0.0

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 12 other files (scripts, references) in awesome-med-research-skills/Data Analysis/differential-expression-analysis of aipoch/medical-research-skills.

  • SKILL.md
  • eval_report_differential-expression-analysis_result.json
  • references/algorithm.md
  • references/cli-guide.md
  • references/troubleshooting.md
  • scripts/diff_methods.R
  • scripts/diff_visualization.R
  • scripts/functions.R
  • scripts/main.R
  • scripts/run_analysis.R
  • scripts/utils.R
  • tests/data/Combined_Datasets_Matrix_mus.csv
  • tests/data/Combined_Datasets_mus_Group.csv

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Differential Expression Analysis next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Differential Expression Analysis compared with similar skills
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Differential Expression Analysis this skillaipoch/medical-research-skills2k—~1.5kAutomated safety check: PassMIT
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Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Differential Expression Analysis

What does Differential Expression Analysis do?

A skill your agent uses when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and…. Differential Expression Analysis is an agent skill from aipoch/medical-research-skills. Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization.

When should I use Differential Expression Analysis?

Differential Expression Analysis fits situations like: analyzing bulk RNA-seq; microarray expression data to identify differentially expressed genes between two biological groups (case vs control); with volcano plots and heatmap visualization.

How do I install Differential Expression Analysis in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill differential-expression-analysis -a claude-code`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/differential-expression-analysis in aipoch/medical-research-skills) into .claude/skills/differential-expression-analysis in your project. Claude Code loads it when a task matches its description.

How do I install Differential Expression Analysis in Codex?

Run `npx skills add aipoch/medical-research-skills --skill differential-expression-analysis -a codex`. Or copy the skill folder (awesome-med-research-skills/Data Analysis/differential-expression-analysis in aipoch/medical-research-skills) into .agents/skills/differential-expression-analysis in your project. Codex loads it when a task matches its description.

Can I use Differential Expression Analysis in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill differential-expression-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/differential-expression-analysis, .gemini/skills/differential-expression-analysis, .github/skills/differential-expression-analysis and .opencode/skills/differential-expression-analysis in your project.

What does Differential Expression Analysis need to run?

Going by SKILL.md and its folder, Differential Expression Analysis needs R for the scripts in its folder.

Does Differential Expression Analysis access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Differential Expression Analysis safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Differential Expression Analysis use?

Differential Expression Analysis is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Differential Expression Analysis use?

About 1.5k tokens (SKILL.md is roughly 6.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.5k tokens, read only when the agent opens those files.

What are the alternatives to Differential Expression Analysis?

Skills that share tags, products or a category with Differential Expression Analysis: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Differential Expression Analysis?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.