Source: https://github.com/aipoch/medical-research-skills

CIBERSORT Immune Infiltration Analysis

When to Use

• Estimate relative immune cell fractions from a bulk expression matrix.
• Compare one case group against one control group after deconvolution.
• Generate structured tables, a serialized result object, and optional PDF plots.

When Not to Use

• Single-cell RNA-seq, spatial transcriptomics, or clustering tasks.
• Absolute clinical interpretation or treatment recommendation.
• Workflows that require the original online CIBERSORT service instead of a local R implementation.

Workflow

1. Confirm that the expression matrix, group file, and signature matrix are available.
2. Run scripts/main.R with the case and control groups.
3. Review the full result table, derived summary tables, and optional plots.
4. Inspect run_record.txt and output_manifest.txt after each run, including failed validation attempts.

When to Read External Files

Situation	File to Read	Purpose
Need to run the analysis	scripts/main.R	CLI entry point
Need algorithm details	references/algorithm.md	HQ reference workflow and result interpretation
Encounter an error	references/troubleshooting.md	Error codes and environment fixes
Need CLI examples or the baseline record	references/cli-guide.md	Example commands and validation notes
Need packaged test inputs	tests/data/	Demo expression matrix, group file, and LM22 file

Usage

Rscript scripts/main.R \
  --input_file ./expression_matrix.csv \
  --group_file ./group_info.csv \
  --signature_file ./LM22.txt \
  --case_group treatment \
  --control_group control \
  --output_dir ./output \
  --qn false \
  --seed 42

Arguments