VisualZoneR: A computational protocol to identify compartmental zones from single-cell spatial transcriptomics using R

Abstract

Summary: VisualZoneR is an R-based technique used to analyze spatial transcriptomics data generated by employing Visium or Visium HD technology. Here, we present a protocol to identify compartmental zones from single-cell spatial transcriptomics using VisualZoneR. We describe steps for identifying distinct zones ranging from healthy liver tissue to inner metastatic areas and measuring transcriptomic changes. We then detail procedures for integrating distinct samples and grouping transcriptomic spots into compartmental zones according to their relative distance from the tumor/liver parenchyma boundary. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Single Cell
• Cancer
• Gene Expression