SpaRGS supporting data: simulation, robustness and spatial transcriptomics analyses

This dataset provides supporting analysis outputs for the manuscript “SpaRGS maps spatial pathway contrasts through directional rank aggregation.” Five archives contain selected results from the manuscript workflows: • simulation.zip: case-level benchmark metrics, GSDensity parameter sensitivity results, saved simulations, and reproducibility metadata.• robustness.zip: directionality-threshold, smoothing-bandwidth, weight-clipping, spatial-graph, and hex-block sensitivity outputs.• breast_visium.zip: processed analysis objects, pathway-score matrices, spatial statistics, cell-type anchoring results, exploratory EnrichMap comparisons, and software-environment records.• DLPFC.zip: processed data and scoring results for twelve cortical sections, recurrence and block-size summaries, and saved randomization objects for representative section 151673.• xenium.zip: pathway-score matrices, processed analysis data, cell metadata, panel coverage, spatial-statistic comparisons, and pathway–module gene-overlap sensitivity results. The accompanying README describes the archive structure, restoration paths, file formats, source datasets, and reproducibility requirements. These files support inspection and reuse of the reported results alongside the associated software and original public inputs. Related software is archived as release v1.1.1-spargs, at https://doi.org/10.5281/zenodo.23894838. Source code and documentation are available at https://github.com/TransBioInfoLab/SpaRGS. Supplementary Data 1–5 and the formatted supplementary figures and tables accompany the manuscript separately and are not bundled in this data record. Original raw datasets should be obtained from the public sources identified in the README and manuscript.