Package: DESpace
Type: Package
Title: DESpace: a framework to discover spatially variable genes and
        differential spatial patterns across conditions
Version: 2.1.0
Description: 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. 
Authors@R: c(
    person(given = "Peiying",
           family = "Cai",
           role = c("aut", "cre"),
           email = "peiying.cai@uzh.ch",
           comment = c(ORCID = "0009-0001-9229-2244")),
    person(given = "Simone",
           family = "Tiberi",
           role = c("aut"),
           email = "simone.tiberi@unibo.it",
           comment = c(ORCID = "0000-0002-3054-9964")))
biocViews: Spatial, SingleCell, RNASeq, Transcriptomics,
        GeneExpression, Sequencing,
        DifferentialExpression,StatisticalMethod, Visualization
License: GPL-3
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
VignetteBuilder: knitr
RoxygenNote: 7.3.2
ByteCompile: true
Encoding: UTF-8
URL: https://github.com/peicai/DESpace,
        https://peicai.github.io/DESpace/
BugReports: https://github.com/peicai/DESpace/issues
git_url: https://git.bioconductor.org/packages/DESpace
git_branch: devel
git_last_commit: d0e41b7
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-05-28
NeedsCompilation: no
Packaged: 2025-05-28 20:11:46 UTC; biocbuild
Author: Peiying Cai [aut, cre] (ORCID: <https://orcid.org/0009-0001-9229-2244>),
  Simone Tiberi [aut] (ORCID: <https://orcid.org/0000-0002-3054-9964>)
Maintainer: Peiying Cai <peiying.cai@uzh.ch>
Built: R 4.5.0; ; 2025-05-29 02:14:26 UTC; unix
