DESpace: a framework to discover spatially variable genes

DESpace is an intuitive framework for identifying spatially variable genes (SVGs) via edgeR, one of the most common methods 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.

Check the vignettes for a description of the main conceptual and mathematical aspects, as well as usage guidelines.

A pre-print will follow shortly.

Bioconductor installation

DESpace is available on Bioconductor and can be installed with the command:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("DESpace")

Vignette

The vignette illustrating how to use the package can be accessed on Bioconductor or from R via:

vignette("DESpace")

or

browseVignettes("DESpace")