Package: DESpace
Type: Package
Title: DESpace: a framework to discover spatially variable genes and
        differential spatial patterns across conditions
Version: 2.2.2
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 (>= 4.4.0)
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: 7.3.3
ByteCompile: true
Encoding: UTF-8
URL: https://github.com/peicai/DESpace,
        https://peicai.github.io/DESpace/
BugReports: https://github.com/peicai/DESpace/issues
Config/pak/sysreqs: libabsl-dev cmake libfontconfig1-dev
        libfreetype6-dev libgdal-dev gdal-bin libgeos-dev
        libmagick++-dev gsfonts libicu-dev libssl-dev libproj-dev
        libsqlite3-dev libudunits2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-28 13:34:46 UTC
RemoteUrl: https://github.com/bioc/DESpace
RemoteRef: RELEASE_3_22
RemoteSha: 1d2c8e9650d282236e2f0020cd062b6c3a7f09d1
NeedsCompilation: no
Packaged: 2025-11-29 04:08:21 UTC; root
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 4.5.2; ; 2025-11-29 04:18:10 UTC; windows
