Spatial Transcriptomics Analysis Pipeline — interactive reports accompanying the STAPLE research article.
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 three complete STAPLE runs: one on a pancreatic ductal adenocarcinoma (PDAC) 10X Visium HD chemoterapy response study cohort, one on a nucleus accumbens (NAc) brain dataset from the GEO accession GSE307586 referenced in the companion data paper, and one on an osteosarcoma Xenium spatial transcriptomics dataset. Each dataset is represented by a MultiQC analysis report (biological results), a Nextflow workflow execution report (pipeline performance) and AI summaries.
Supplementary Figures & Reports
Interactive MultiQC report summarising cell-type deconvolution, spatial neighborhood, ligand-receptor interactions, and Moran's I spatial autocorrelation statistics across PDAC tissue sections.
↗Nextflow execution report for the PDAC STAPLE run: per-process resource usage, CPU and memory consumption, task timeline, and pipeline DAG.
↗AI-generated research on the mechanisms of response resistance for the PDAC STAPLE run.
↗AI-generated perturbation agent follow-up research based on the proposed mechanisms of response resistance.
↗Interactive MultiQC report summarising quality control, cell-type deconvolution, cell type neighborhoods, ligand-receptor interactions, and Moran's I spatial autocorrelation statistics across NAc tissue sections.
↗Nextflow execution report for the NAc STAPLE run: per-process resource usage, CPU and memory consumption, task timeline, and pipeline DAG.
↗AI-generated summary comparing key findings and insights for the NAc STAPLE run VS original NAc paper.
↗Interactive MultiQC report summarising cell-type deconvolution, spatial neighborhoods, ligand-receptor interactions, and spatial statistics for osteosarcoma Xenium tissue sections.
↗Nextflow execution report for the osteosarcoma STAPLE run: per-process resource usage, CPU and memory consumption, task timeline, and pipeline DAG.
↗AI-generated summary and analysis of the osteosarcoma STAPLE run with Xenium spatial transcriptomics data.
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