Package: SpotSweeper
Title: Spatially-aware quality control for spatial transcriptomics
Version: 1.9.2
Date: 2026-09-08
Authors@R: c(
    person("Michael", "Totty", email = "mictott@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-9292-8556")),
    person("Stephanie", "Hicks", email = "shicks19@jhu.edu", role = c("aut"),
           comment = c(ORCID = "0000-0002-7858-0231")),
    person("Boyi", "Guo", email = "boyi.guo.work@gmail.com", role = c("aut"),
           comment = c(ORCID = "0000-0003-2950-2349")))
Description: Spatially-aware quality control (QC) software for both
        spot-level and artifact-level QC in spot-based spatial
        transcriptomics, such as 10x Visium. These methods calculate
        local (nearest-neighbors) mean and variance of standard QC
        metrics (library size, unique genes, and mitochondrial
        percentage) to identify outlier spots and large technical
        artifacts.
License: MIT + file LICENSE
URL: https://github.com/MicTott/SpotSweeper
BugReports: https://support.bioconductor.org/tag/SpotSweeper
biocViews: Software, Spatial, Transcriptomics, QualityControl,
        GeneExpression,
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.4.0)
Imports: SpatialExperiment, SummarizedExperiment, S4Vectors,
        BiocNeighbors, SingleCellExperiment, stats, escheR, MASS,
        ggplot2, grDevices, BiocParallel
Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr,
        testthat (>= 3.0.0), SeuratObject, Seurat
Config/testthat/edition: 3
VignetteBuilder: knitr
LazyData: False
News: NEWS.md
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-08 22:19:06 UTC
RemoteUrl: https://github.com/bioc/SpotSweeper
RemoteRef: HEAD
RemoteSha: 7717432f8ad9ed0bdec51b0f637917e6ac6887a3
NeedsCompilation: no
Packaged: 2026-09-09 14:53:31 UTC; root
Author: Michael Totty [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9292-8556>),
  Stephanie Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>),
  Boyi Guo [aut] (ORCID: <https://orcid.org/0000-0003-2950-2349>)
Maintainer: Michael Totty <mictott@gmail.com>
Built: R 4.6.1; ; 2026-09-09 15:00:17 UTC; windows
