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estimate-immune-score-analysis

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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.

When to use

• 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
• "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"

When not to use

• Immune cell fraction estimation: use a CIBERSORT-like deconvolution workflow instead
• Differential testing between biological groups: use a differential analysis skill instead
• Single-cell analysis: use a single-cell-specific workflow
• Clinical diagnosis or treatment decision support: do not use this skill

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