AgentSkillsCN

Skill: TCGA LUAD/LUSC pipeline

技能：TCGA LUAD/LUSC管道

SKILL.md

Skill: TCGA LUAD/LUSC pipeline

Purpose

Fetch expression/clinical data via GDC and cBioPortal; compute correlations, survival curves, and immune infiltration proxies; produce figures.

Inputs

  • •Gene list (e.g., SQSTM1, CD274, HIP1R, CMTM6, STUB1).

Outputs

  • •outputs/tcga/*.csv, figures/tcga/*, outputs/tcga/summary.md.

Steps

  1. •GDC: query and download expression + clinical for LUAD/LUSC.
  2. •Correlation (Pearson/Spearman), KM survival (median split), Cox multivariate.
  3. •Optional: immune infiltration scores (ESTIMATE‑like proxy if no deconvolution available).