Φ-Space: Continuous phenotyping of single-cell and spatial omics data.

Vignettes

PhiSpace pkgdown site

A workflow for spatial transcriptomics featuring SpaNorm, PhiSpace and jazzPanda

Installation

if(!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install('jiadongm/PhiSpace/pkg')

Citing PhiSpace

Mao, Jiadong, Choi, Jarny and Lê Cao, Kim-Anh. (2026). Φ-Space ST: a platform-agnostic method to identify cell states in spatial transcriptomics studies. Cell Reports Methods 6(8), 101483. doi:10.1016/j.crmeth.2026.101483.

Mao, Jiadong, Deng, Yidi and Lê Cao, Kim-Anh. (2025). Φ-Space: continuous phenotyping of single-cell multi-omics data. Genome Biology 26, 323. doi:10.1186/s13059-025-03755-8.