cibersort-immune-infiltration-analysis

1> **Source**: [https://github.com/aipoch/medical-research-skills](https://github.com/aipoch/medical-research-skills)
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3# CIBERSORT Immune Infiltration Analysis
4 
5## When to Use
6 
7- Estimate relative immune cell fractions from a bulk expression matrix.
8- Compare one case group against one control group after deconvolution.
9- Generate structured tables, a serialized result object, and optional PDF plots.
10 
11## When Not to Use
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13- Single-cell RNA-seq, spatial transcriptomics, or clustering tasks.
14- Absolute clinical interpretation or treatment recommendation.
15- Workflows that require the original online CIBERSORT service instead of a local R implementation.
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17## Workflow
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191. Confirm that the expression matrix, group file, and signature matrix are available.
202. Run `scripts/main.R` with the case and control groups.
213. Review the full result table, derived summary tables, and optional plots.
224. Inspect `run_record.txt` and `output_manifest.txt` after each run, including failed validation attempts.
23 
24## When to Read External Files
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26| Situation | File to Read | Purpose |
27|-----------|--------------|---------|
28| Need to run the analysis | `scripts/main.R` | CLI entry point |
29| Need algorithm details | `references/algorithm.md` | HQ reference workflow and result interpretation |
30| Encounter an error | `references/troubleshooting.md` | Error codes and environment fixes |
31| Need CLI examples or the baseline record | `references/cli-guide.md` | Example commands and validation notes |
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