Package: spacexr
Type: Package
Title: SpatialeXpressionR: Cell Type Identification in Spatial
        Transcriptomics
Version: 1.2.0
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: RELEASE_3_22
git_last_commit: b6d81f6
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 06:38:18 UTC; biocbuild
Author: Dylan Cable [aut],
  Rafael Irizarry [aut] (ORCID: <https://orcid.org/0000-0002-3944-4309>),
  Gabriel Grajeda [cre] (ORCID: <https://orcid.org/0009-0003-7242-7476>),
  Fannie and John Hertz Foundation [fnd]
Maintainer: Gabriel Grajeda <gabriel.grajeda@gmail.com>
