DOI: 10.18129/B9.bioc.DESpace  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DESpace.

DESpace: a framework to discover spatially variable genes

Bioconductor version: 3.17

Intuitive framework for identifying spatially variable genes (SVGs) 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. The method is flexible and robust, and is faster than the most SV methods. Furthermore, to the best of our knowledge, it is the only SV approach that allows: - performing a SV test on each individual spatial cluster, hence identifying the key regions of the tissue affected by spatial variability; - jointly fitting multiple samples, targeting genes with consistent spatial patterns across replicates.

Author: Peiying Cai [aut, cre] , Simone Tiberi [aut, cte]

Maintainer: Peiying Cai <peiying.cai at>

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biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Spatial, StatisticalMethod, Transcriptomics, Visualization
Version 1.0.0
In Bioconductor since BioC 3.17 (R-4.3) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports edgeR, limma, dplyr, stats, Matrix, SpatialExperiment, ggplot2, ggpubr, scales, SummarizedExperiment, S4Vectors, BiocGenerics, data.table, assertthat, cowplot, ggforce, ggnewscale, patchwork, BiocParallel, methods
Suggests knitr, rmarkdown, testthat, BiocStyle, ExperimentHub, concaveman, spatialLIBD, purrr, scuttle, utils
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