This repository contains code used to perform analysis and figures featured in our paper: Spotlight on 10x Visium: a multi-sample protocol comparison of spatial technologies
Mei R. M. Du, Changqing Wang, Charity W. Law, Daniela Amann-Zalcenstein, Casey J. A. Anttila, Ling Ling, Peter F. Hickey, Callum J. Sargeant, Yunshun Chen, Lisa J. Ioannidis, Pradeep Rajasekhar, Raymond Yip, Kelly L. Rogers, Diana S. Hansen, Rory Bowden, and Matthew E. Ritchie
Figure created with BioRender.
Our processed Visium and 10x scRNA-seq datasets, along with the code are available from zenodo: 
Please cite our paper if you use our data and/or scripts in your studies.
Code to produce the reports are stored as Rmarkdown documents in analysis. Objects are saved in output.
Sample 709 FFPE CA: analysis/EDA_709_FFPE_CA.Rmd
Sample 713 FFPE CA: analysis/EDA_713_FFPE_CA.Rmd
analysis/sc_preprocessing.Rmd
Multi-sample feature selection, clustering, cell type deconvolution: analysis/FFPE_CA_multi-sample.Rmd
Pseudo-bulk differential expression analysis: as targets project under the targets_project folder
Simply navigate to the targets_project folder from the zenodo tarball SpatialBenchVisium.tar.gz and run targets::tar_make() to run the entire pipeline, outputs are saved in the targets_project/output folder.
Figures 1-3, Supplementary figures S2-S7: analysis/figures.R
Figure 4 & 5, Supplementary figures S8-S11: run targets::tar_make() in the targets_project folder, figures are saved to targets_project/output