DESpace

DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

Bioconductor version: 3.23 · Package version: 2.4.0

Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESpace")