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

ssGSEA Immune Infiltration Analysis

When to Use

• Estimate relative immune infiltration from a bulk RNA-seq expression matrix.
• Compare immune enrichment scores between one case group and one control group.
• Generate structured result tables plus optional PDF visualizations for downstream review.

When Not to Use

• Single-cell RNA-seq or spatial transcriptomics.
• Absolute immune cell proportion estimation or deconvolution.
• Clinical diagnosis, treatment recommendation, or any other medical decision making.

Workflow