# DESpace: a framework to discover spatially variable genes <img src="inst/extdata/DESpace.png" width="200" align="right"/> `DESpace` is an intuitive framework for identifying spatially variable genes (SVGs) via [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html), 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](https://bioconductor.org/packages/release/bioc/html/edgeR.html), 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](https://bioconductor.org/packages/DESpace) and can be installed with the command: ``` r 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](https://bioconductor.org/packages/DESpace) or from R via: ``` r vignette("DESpace") ``` or ``` r browseVignettes("DESpace") ```