Online Resource 2 | Metabolomics
Acute kidney injury is associated with less reversal of urinary metabolomic changes after coronary artery bypass grafting
Authors: Donglin Xu, Zengkun Liu, Haixuan Zhao, Ang Li, Qiduo Chen, Jing Liu, Hourong Sun
Corresponding author: Hourong Sun; Department of Cardiovascular Surgery, Qilu Hospital of Shandong University, 107 Wenhua Xi Road, Jinan, Shandong 250012, China; Email: sunhourong2016@126.com; Tel.: +86-185-6008-6790

CONTENTS
Analysis_Code.R — the original supplied analysis script, byte-for-byte unchanged.
SHA-256: e78969ac3a1a3936a287317acfd96bdfb8fd743b5ac8a98d4c3c948b8dd65bb0

REQUIREMENTS
R 4.4.1; packages readxl, openxlsx and Rcpp; a compatible Rtools toolchain on Windows.

PUBLIC INPUTS
pr5c00113_si_002.xlsx (Zhao Table S1, AKI)
pr5c00113_si_003.xlsx (Zhao Table S2, non-AKI)
11306_2026_2423_MOESM2_ESM.xlsx (Lee Supplementary Material 2; fill0.5min worksheet)
Stage13_GSE183276/GSE183276_Kidney_Healthy-Injury_Cell_Atlas_scCv3_Metadata_03282022.txt.gz
The original processed matrices are not redistributed. See Online Resource 1, Table S5, and the manuscript data-availability statement for source records.

RUN
Set CSA_AKI_DATA_DIR and CSA_AKI_OUTPUT_DIR before invoking Rscript --vanilla Analysis_Code.R.
An optional CSA_AKI_KPMP_FILE environment variable can override the metadata-file location.
The two PATH_TO_* values in the script are intentional user-configuration defaults; environment variables override them without editing the script.

OUTPUT
CSA_AKI_manuscript_reproduction.xlsx contains calculated patient scores, statistical summaries, quality-control checks and session information. The script also uses a cpp_cache directory. Full permutations may take substantial computation time.

PROTOCOL AND INTERPRETATION
The computational sequence is documented in Online Resource 5. Raw mass-spectrometry files are not reprocessed. Inference uses patients, not independent samples or cells. The separate urine cohort and kidney atlas do not replicate longitudinal return to baseline.

This journal-formatting revision did not rerun the statistical analyses.
