Package: SpatialArtifacts
Title: Identification and Classification of Spatial Artifacts in Visium
        and Visium HD Data
Version: 1.0.0
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
Config/pak/sysreqs: libgdal-dev gdal-bin libgeos-dev libmagick++-dev
        gsfonts libicu-dev libssl-dev libproj-dev libsqlite3-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:47 UTC
RemoteUrl: https://github.com/bioc/SpatialArtifacts
RemoteRef: RELEASE_3_23
RemoteSha: df87fa085a707d8c05cd080def34907dec63d2ef
NeedsCompilation: no
Packaged: 2026-04-30 06:35:51 UTC; root
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; ; 2026-04-30 06:45:20 UTC; windows
