VisualZoneR: A computational protocol to identify compartmental zones from single-cell spatial transcriptomics using R.
STAR Protoc
; 5(3): 103196, 2024 Sep 20.
Article
em En
| MEDLINE
| ID: mdl-39067026
ABSTRACT
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Limite:
Humans
Idioma:
En
Ano de publicação:
2024
Tipo de documento:
Article