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