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Updated: May 4, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
Published on: January 10, 2019
VisualZoneR: A computational protocol to identify compartmental zones from single-cell spatial transcriptomics using
Thomas Kerzel1, Stefano Beretta1, Luigi Naldini2
1San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
None:
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.
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