estimate-immune-score-analysis

1# ESTIMATE Immune Score Analysis
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3## When to Use
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5Use this skill when the user wants to:
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7- compute ESTIMATE-derived immune and stromal scores from a bulk expression matrix
8- transform an expression matrix into `estimate` package input files and score outputs
9- generate an ESTIMATE score heatmap across samples
10- compare ESTIMATE scores across sample groups when a sample group file is available
11- create a reproducible CLI-backed ESTIMATE workflow with structured output records
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13Typical request patterns:
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15- "Run ESTIMATE immune score analysis on this expression matrix"
16- "Calculate ImmuneScore and StromalScore from my bulk RNA-seq data"
17- "Generate ESTIMATE scores and save a sample-level result table"
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19## Execution Model
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21This is a CLI-backed analysis skill.
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231. Use `SKILL.md` to confirm that the task is ESTIMATE score generation from bulk expression data.
242. Use `scripts/main.R` for the real execution.
253. Provide one expression matrix file with genes in the first column and samples in the remaining columns.
264. Optionally provide a sample group file to generate ESTIMATE score boxplots and a significance summary table.
275. The workflow always generates an ESTIMATE score heatmap from the computed score table.
286. Read reference files only when you need algorithm details, troubleshooting, or baseline execution notes.
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30## When to Read External Files
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32| Situation | File to Read | Purpose |
33|-----------|--------------|---------|
34…