Package: spacexr
Type: Package
Title: SpatialeXpressionR: Cell Type Identification in Spatial
        Transcriptomics
Version: 1.5.0
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
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev make
        libmagick++-dev gsfonts libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:04:48 UTC
RemoteUrl: https://github.com/bioc/spacexr
RemoteRef: HEAD
RemoteSha: b981b934b5bb557afd4f60a38deacf80acfcfa9d
NeedsCompilation: no
Packaged: 2026-07-14 05:09:35 UTC; root
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>