Supplementary Code for Scientific Reports submission

Manuscript: A single-cell-informed T-cell exhaustion-associated immune microenvironment signature for lung adenocarcinoma prognosis

Files
- 01_main_reproducibility_script_as_uploaded.R: R script text extracted from the author-provided code document. It contains the main analysis workflow used for single-cell preprocessing, TCGA model construction, external GSE72094 evaluation, functional and immune analyses, and supplementary revision analyses.

How to use
1. Create a local project directory with subfolders 01_RawData, 02_ProcessedData, 03_Results, and 04_Logs.
2. Place the public datasets described in the manuscript into 01_RawData or allow the script sections that use GEOquery/TCGAbiolinks to download public data where applicable.
3. Update the project root at the beginning of the script if your local path is not D:/rstudio/t1.
4. Run the code stepwise in R/RStudio rather than all at once, because the workflow downloads public data, writes intermediate objects, and expects intermediate files produced by earlier sections.

Notes
- No patient-level private data are included in this code package.
- Raw TCGA and GEO datasets are not redistributed here because they are publicly available from the repositories listed in the manuscript Data availability statement.
- The script preserves the analysis logic and local directory structure used by the authors; users may need to adjust file paths for their own computing environment.
