Skills for Real Engineers. Straight from my .agents directory.
39 skills
differential-expression-analysis
Agent skill from
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.
How to install differential-expression-analysis
install differential-expression-analysis
# install the medical-research-skills pack with the skills CLI
npx skills add aipoch/medical-research-skills# or add only this skill to Claude Code: copy the folder
awesome-med-research-skills/Data Analysis/differential-expression-analysis/
# into
~/.claude/skills/differential-expression-analysis/ (all projects)
.claude/skills/differential-expression-analysis/ (one project)
1> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)23# Differential Expression Analysis45## When to Read External Files67| Situation | File to Read | Purpose |8|-----------|--------------|---------|9| **Need algorithm details** | `references/algorithm.md` | Statistical methods, formulas, assumptions |10| **Need to run analysis** | `scripts/main.R` | Execute: `Rscript scripts/main.R --input_file ... --group_file ...` |11| **Encounter errors** | `references/troubleshooting.md` | Common errors and solutions |12| **Need CLI examples** | `references/cli-guide.md` | Detailed CLI usage examples |13| **Need test data** | `tests/data/` | Sample input files for testing |1415---1617## Usage1819```bash20Rscript scripts/main.R \21 --input_file ./expression_matrix.csv \22 --group_file ./group_info.csv \23 --output_dir ./output/ \24 --diff_method limma \25 --p_threshold 0.05 \26 --logfc_threshold 0.1 \27 --seed 4228```2930---3132## Arguments3334| Short | Long | Type | Default | Description |35|-------|------|------|---------|-------------|36| `-i` | `--input_file` | character | **required** | Expression matrix file (genes as rows, samples as columns) |37| `-g` | `--group_file` | character | **required** | Group information file (sample ID + group columns) |38| `-o` | `--output_dir` | character | `./output/` | Output directory |39| `-m` | `--diff_method` | character | `limma` | Method: limma, deseq2, edger, t, wilcox |40…
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