# Estimate Immune Score Analysis

Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk...

- Repository: https://github.com/aipoch/medical-research-skills (2020 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-09-17
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add aipoch/medical-research-skills --skill estimate-immune-score-analysis -g -a claude-code -y`
Codex: `npx skills add aipoch/medical-research-skills --skill estimate-immune-score-analysis -g -a codex -y`
Cursor: `npx skills add aipoch/medical-research-skills --skill estimate-immune-score-analysis -g -a cursor -y`
Gemini CLI: `npx skills add aipoch/medical-research-skills --skill estimate-immune-score-analysis -g -a gemini-cli -y`

## Description

Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots plus significance tables when a sample group file is supplied. Trigger keywords: ESTIMATE, immune score, stromal score, tumor microenvironment score. NOT for: immune cell deconvolution, single-cell analysis, differential expression, clinical diagnosis.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# ESTIMATE Immune Score Analysis

## When to Use

Use this skill when the user wants to:

- compute ESTIMATE-derived immune and stromal scores from a bulk expression matrix
- transform an expression matrix into `estimate` package input files and score outputs
- generate an ESTIMATE score heatmap across samples
- compare ESTIMATE scores across sample groups when a sample group file is available
- create a reproducible CLI-backed ESTIMATE workflow with structured output records

Typical request patterns:

- "Run ESTIMATE immune score analysis on this expression matrix"
- "Calculate ImmuneScore and StromalScore from my bulk RNA-seq data"
- "Generate ESTIMATE scores and save a sample-level result table"

## Execution Model

This is a CLI-backed analysis skill.

1. Use `SKILL.md` to confirm that the task is ESTIMATE score generation from bulk expression data.
2. Use `scripts/main.R` for the real execution.
3. Provide one expression matrix file with genes in the first column and samples in the remaining columns.
4. Optionally provide a sample group file to generate ESTIMATE score boxplots and a significance summary table.
5. The workflow always generates an ESTIMATE score heatmap from the computed score table.
6. Read reference files only when you need algorithm details, troubleshooting, or baseline execution notes.

## When to Read External Files

| Situation | File to Read | Purpose |
|-----------|--------------|---------|
| Need algorithm details | `references/algorithm.md` | Understand the ESTIMATE scoring workflow and result interpretation |
| Need to run the skill | `scripts/main.R` | Execute the CLI entry point |
| Encounter errors | `references/troubleshooting.md` | Find standard error codes and fixes |
| Need more CLI examples or the real-data baseline record | `references/cli-guide.md` | Copy commands and review the recorded execution template |
| Need sample input files | `tests/data/` | Use the bundled demo expression matrix |

## When Not to Use

The rest: https://github.com/aipoch/medical-research-skills/blob/HEAD/awesome-med-research-skills/Data Analysis/estimate-immune-score-analysis/SKILL.md