Reproducibility package for: Cross-cohort single-cell localisation of an early-recurrence-associated transcriptional program in intrahepatic cholangiocarcinoma

This archive contains the analysis scripts, derived non-source result tables, figures, and supplementary tables supporting the manuscript “Cross-cohort single-cell localisation of an early-recurrence-associated transcriptional program in intrahepatic cholangiocarcinoma”. The study reanalysed publicly available transcriptomic datasets from GEO (GSE107943, GSE138709, and GSE151530). No new human-participant data or identifiable information are included. Raw GEO files are not redistributed; the README specifies the required source files, directory layout, software environment, and reproduction order. The analysis localises a locked early-recurrence-associated bulk transcriptional program to myeloid/tumour-associated macrophage compartments across two iCCA single-cell cohorts. It does not establish causality, a therapeutic target, a universal macrophage subtype, spatial interaction, or a virtual gene-perturbation result.