DESpace
This is the development version of DESpace; for the stable release version, see DESpace.
All Bioconductor versions of DESpace
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17
DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Bioconductor version: 3.24 · Package version: 2.5.0
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.
Author: Peiying Cai [aut, cre] 
, Simone Tiberi [aut]
Maintainer: Peiying Cai <peiying.cai at uzh.ch>
Citation
From within R, enter citation("DESpace"):
Peiying Cai, Simone Tiberi. DESpace: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions. doi:10.18129/B9.bioc.DESpace, R package version 2.5.0, https://bioconductor.org/packages/DESpace.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DESpace")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.5.0 |
| License | GPL-3 |
| URL | https://github.com/peicai/DESpace https://peicai.github.io/DESpace/ |
| Bug Reports | https://github.com/peicai/DESpace/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3 years) |
| Downloads rank | 957 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Spatial, StatisticalMethod, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/DESpace/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DESpace")| A framework to discover Spatially Variable genes via spatial clusters | HTML | R Script |
| Differential Spatial Pattern between conditions | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | DESpace_2.5.0.tar.gz |
| Windows binary (x86_64) | DESpace_2.5.0.zip |
| macOS binary (arm64) | DESpace_2.5.0.tgz |
| macOS binary (x86_64) | DESpace_2.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DESpace |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DESpace |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, terra, sf, spatstat.explore, spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel, methods, scales, scuttle
Suggests: knitr, rmarkdown, testthat, BiocStyle, muSpaData, ExperimentHub, spatialLIBD, purrr, reshape2, tidyverse, concaveman