Package: SpatialArtifacts
Title: Identification and Classification of Spatial Artifacts in Visium
        and Visium HD Data
Version: 0.99.10
Authors@R: 
    c(person("Harriet Jiali", "He", email = "jhe46@jh.edu", role = c("aut", "cre"), comment = c(ORCID = "0009-0003-7827-2735")),
      person("Jacqueline R.", "Thompson", email = "jthom338@jh.edu", role = "aut"),
      person("Michael", "Totty", email = "mtotty2@jh.edu", role = "aut"),
      person("Stephanie C.", "Hicks", email = "shicks19@jhu.edu", role = c("aut", "fnd"), comment = c(ORCID = "0000-0002-7858-0231")))
Description: SpatialArtifacts provides a data-driven two-step workflow to identify, 
    classify, and handle spatial artifacts in spatial transcriptomics data. The 
    package combines median absolute deviation (MAD)-based outlier detection 
    with morphological image processing (fill, outline, and star patterns) to 
    detect edge and interior artifacts. It supports multiple platforms including 
    10x Genomics Visium (standard and HD), allowing for consistent quality 
    control across different spatial resolutions.
Depends: R (>= 4.4.0)
License: Artistic-2.0
URL: https://github.com/CambridgeCat13/SpatialArtifacts
BugReports: https://github.com/CambridgeCat13/SpatialArtifacts/issues
biocViews: Software, Spatial, Transcriptomics, QualityControl,
        DataImport, WorkflowStep, Classification
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
SystemRequirements: quarto, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>=
        4.8.0)
VignetteBuilder: knitr
Imports: SpatialExperiment, SummarizedExperiment, S4Vectors, scuttle,
        dplyr, terra, stats, methods
Suggests: BiocStyle, knitr, rmarkdown, BiocCheck, ggplot2, patchwork,
        testthat (>= 3.0.0)
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/SpatialArtifacts
git_branch: devel
git_last_commit: a41ea39
git_last_commit_date: 2026-04-19
Repository: Bioconductor 3.23
Date/Publication: 2026-04-20
NeedsCompilation: no
Packaged: 2026-04-20 21:59:33 UTC; biocbuild
Author: Harriet Jiali He [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-7827-2735>),
  Jacqueline R. Thompson [aut],
  Michael Totty [aut],
  Stephanie C. Hicks [aut, fnd] (ORCID:
    <https://orcid.org/0000-0002-7858-0231>)
Maintainer: Harriet Jiali He <jhe46@jh.edu>
Built: R 4.6.0; ; 2026-04-21 03:39:38 UTC; unix
