Package: spacexr
Type: Package
Title: SpatialeXpressionR: Cell Type Identification in Spatial Transcriptomics
Version: 1.3.0
Authors@R: c(
    person("Dylan", "Cable", email = "dmcable@umich.edu", role = "aut"),
    person(
        "Rafael", "Irizarry", email="rafael_irizarry@dfci.harvard.edu",
        role="aut", comment=c(ORCID="0000-0002-3944-4309")
    ),
    person(
        "Gabriel", "Grajeda", email = "gabriel.grajeda@gmail.com", role = "cre",
        comment=c(ORCID="0009-0003-7242-7476")
    ),
    person("Fannie and John Hertz Foundation", role = "fnd")
    )
Description: Spatial-eXpression-R (spacexr) is a package for analyzing cell
    types in spatial transcriptomics data. This implementation is a fork of the
    spacexr GitHub repo (https://github.com/dmcable/spacexr), adapted to work
    with Bioconductor objects. The original package implements two statistical
    methods: RCTD for learning cell types and CSIDE for inferring cell
    type-specific differential expression. Currently, this fork only implements
    RCTD, which learns cell type profiles from annotated RNA sequencing
    (RNA-seq) reference data and uses these profiles to identify cell types in
    spatial transcriptomic pixels while accounting for platform-specific
    effects. Future releases will include an implementation of CSIDE.
URL: https://github.com/ggrajeda/spacexr
BugReports: https://github.com/ggrajeda/spacexr/issues
Depends: R (>= 4.5.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: 
    ggplot2,
    Matrix,
    parallel,
    quadprog,
    httr,
    methods,
    memoise,
    BiocParallel,
    BiocFileCache,
    SummarizedExperiment,
    scatterpie,
    SpatialExperiment
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat
Config/testthat/edition: 3
biocViews: GeneExpression, DifferentialExpression, SingleCell, RNASeq, Software,
    Spatial, Transcriptomics
git_url: https://git.bioconductor.org/packages/spacexr
git_branch: devel
git_last_commit: ea2a493
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
