snMultiome Gastric WNT Pipeline

A comprehensive 10X Genomics snMultiome (joint snRNA-seq + scATAC-seq) analysis pipeline for reproducing the results from 'Epithelial WNT secretion drives niche escape of developing gastric cancer'. The pipeline processes wild-type (RZ) and KRAS-mutant (RZK) mouse gastric tissue samples through QC filtering, MACS2 peak calling, SCTransform + TF-IDF normalisation, SCT-based integration, UMAP clustering, differential expression (MAST), differential accessibility (LR test), KRAS signaling gene set overlap, and JASPAR2020 TF motif enrichment analysis. Generates publication-quality figures including UMAP plots, DotPlots, dittoBarPlots, FeaturePlots, and motif enrichment bar plots.