Reproducibility package for: From environmental lead exposure to colorectal cancer: integrated transcriptomic and genetic analyses identify HMOX1 as a prioritized candidate

This archive contains the cleaned reproducibility package for the manuscript “From environmental lead exposure to colorectal cancer: integrated transcriptomic and genetic analyses identify HMOX1 as a prioritized candidate”. The package includes executable code, input files, source tables, generated outputs, logs, checksums, and contract tests for the NHANES analysis, GEO preprocessing and differential expression analysis, machine-learning analysis, single-cell and CellChat analyses, MR source-table checks and figure generation, and molecular docking provenance checks. The top-level runner is `run_all.sh`. It creates required output directories, checks input files, runs the major analysis modules in the order described in the README, saves stdout/stderr logs, records session/software information, and writes checksums for generated tables, figures, and CSV files. The run status is recorded in `outputs/logs/run_all_status.csv`. Large public raw files that are not redistributed in full, including the 1000 Genomes LD reference files required for a full raw MR rerun and the original large single-cell raw matrix, are described in the corresponding README files with acquisition instructions. The submitted archive contains the processed Seurat/CellChat objects and source tables needed to check and regenerate the submitted figures and tables.