STAPLE

STAPLE is a Nextflow bioinformatics pipeline for 10× Visium and Visium HD spatial transcriptomics data that puts the scientific question first. Per-sample spatial features — including cell-type deconvolution, cell type spatial composition, and ligand-receptor interaction scoring — are computed and then contrasted across samples using metadata from a samplesheet. Results are aggregated into interactive MultiQC reports optimised for downstream analysis and compatible with LLM-assisted interpretation.

The supplements below document two complete STAPLE runs: one on a pancreatic ductal adenocarcinoma (PDAC) 10X Visium HD chemoterapy response study cohort and one on a nucleus accumbens (NAc) brain dataset from the GEO accession GSE307586 referenced in the companion data paper. Each dataset is represented by a MultiQC analysis report (biological results), a Nextflow workflow execution report (pipeline performance) and AI summaries.