Individual skill
immune-pathway-analysis
Run immune pathway GSVA or ssGSEA analysis from a bulk expression matrix, a sample group file, and a local immune Reactome gene-set table, then export differential pathway results and a heatmap for two-group comparison.
awesome-med-research-skills/Data Analysis/immune-pathway-analysis/SKILL.md
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- Last checked
- Nov 9, 2026
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- 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 · 12,009 bytesSKILL.mdcore · 12,009 byteseval_report_immune-pathway-analysis_result.jsonasset · 14,238 bytesreferences/algorithm.mddoc · 3,512 bytesreferences/cli-guide.mddoc · 6,382 bytesreferences/troubleshooting.mddoc · 6,422 bytesscripts/cli_options.Rruns · 7,211 bytesscripts/functions.Rruns · 5,878 bytesscripts/io.Rruns · 4,213 bytesscripts/main.Rruns · 4,645 bytesscripts/plot_helpers.Rruns · 1,227 bytesscripts/recording.Rruns · 3,560 bytesscripts/run_analysis.Rruns · 3,179 bytesscripts/utils.Rruns · 5,238 bytesscripts/visualization.Rruns · 2,521 bytestests/data/expression_matrix.csvasset · 40,163 bytestests/data/group_info.csvasset · 202 bytestests/data/immune_genesets.csvasset · 2,184,512 bytestests/data/immune_genesets_minimal.csvasset · 530 bytestests/run_tests.Rruns · 2,627 bytestests/run_unit_tests.Rruns · 5,323 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
# Immune Pathway Analysis
## When to Use
Use this skill when the goal is to quantify immune-related pathway activity from bulk expression data and compare pathway enrichment between two sample groups.
Typical requests:
- "Run immune pathway GSVA for these samples."
- "Score immune Reactome pathways and compare case versus control."
- "Generate an immune pathway heatmap from a saved result."
- "Use a local immune gene-set table for pathway scoring."
