Individual skill
estimate-immune-score-analysis
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.
awesome-med-research-skills/Data Analysis/estimate-immune-score-analysis/SKILL.md
Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91
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- Observed behavior
- Local scripts
- Last checked
- Nov 9, 2026
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- 2,042
- Repository last updated
- Sep 17, 2026
- License
- MIT
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- engineering Derived category
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SKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 bytesSKILL.mdcore · 12,533 byteseval_report_estimate-immune-score-analysis_result.jsonasset · 13,412 bytesreferences/algorithm.mddoc · 2,552 bytesreferences/cli-guide.mddoc · 6,212 bytesreferences/troubleshooting.mddoc · 4,280 bytesscripts/cli_options.Rruns · 3,672 bytesscripts/functions.Rruns · 5,657 bytesscripts/io.Rruns · 2,422 bytesscripts/main.Rruns · 3,909 bytesscripts/recording.Rruns · 4,136 bytesscripts/run_analysis.Rruns · 2,616 bytesscripts/utils.Rruns · 4,882 bytesscripts/visualization.Rruns · 6,731 bytestests/data/expression_matrix.csvasset · 40,163 bytestests/data/group_info.csvasset · 202 bytestests/run_tests.Rruns · 868 bytes
Read excerpt
# 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:
