This repository contains the code to reproduce the analysis in:
Li M*, Liu N*, Nguyen QH, Chen Y (2025). Preserving tissue structure through density-based spatial analysis with scider. bioRxiv https://doi.org/10.1101/2025.09.11.675745.
The Xenium data is available as GEO series GSE243168.
The Cell type annotation is obtained from 10x Genomics.
The code for generating the figures in the paper is in Xenium.
The Visium HD data is available at the 10x Genomics
The code for generating the figures in the paper is in visiumHD.