supplementary file of "Single-Cell Identification of Malignant Epithelial Programs and Tumor-Immune Communication Networks in a China-Based Pancreatic Ductal Adenocarcinoma Cohort"

Supplementary data and analysis archive for the manuscript "Single-Cell Identification of Malignant Epithelial Programs and Tumor-Immune Communication Networks in a China-Based Pancreatic Ductal Adenocarcinoma Cohort" (Zeliang Xia et al.). This archive supports a secondary analysis of publicly available pancreatic ductal adenocarcinoma (PDAC) single-cell RNA sequencing data. No new sequencing data were generated in this study. Primary data sources Discovery cohort: CRA001160, Genome Sequence Archive, National Genomics Data Center. Processed objects: Figshare, DOI 10.6084/m9.figshare.14308526. External validation and spatial transcriptomics: GSE111672, NCBI Gene Expression Omnibus. Contents of this archive Supplementary Tables S1a-S1e and S2-S19, covering gene module definitions, the 44-pair communication panel, cross-cohort gene effects, gene-symbol harmonization, PDAC-C label-transfer validation, expression-inferred sex sensitivity, post hoc count-level QC, and spatial sensitivity results. Main Tables 1-5 and Figures 1-7 as individual files. Machine-readable intermediate outputs, including post hoc count-level QC metrics for CRA001160 and GSE111672, the externally derived malignancy signature results, module and NMF program analyses, and spatial edge summaries. Analysis code in Python, with parameter settings and the fixed random seed, requirements.txt, SHA256SUMS.txt, README.txt, AUDIT_REPORT.txt, the source manifest DATA_SOURCE_MANIFEST.csv, and a manuscript-to-archive crosswalk MANUSCRIPT_TO_ARCHIVE_CROSSWALK.csv.