Package: SpotClean
Version: 1.12.1
Date: 2026/02/03
Title: SpotClean adjusts for spot swapping in spatial transcriptomics
        data
Authors@R: c(
    person("Zijian", "Ni", email="zni25@wisc.edu", role = c("aut", "cre"), 
        comment = c(ORCID = "0000-0003-1181-8337")),
    person("Christina", "Kendziorski", role = "ctb")
  )
Depends: R (>= 4.2.0),
Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment,
        SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap,
        rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils,
        spelling
biocViews: DataImport, RNASeq, Sequencing, GeneExpression, Spatial,
        SingleCell, Transcriptomics, Preprocessing
Description: SpotClean is a computational method to adjust for spot
        swapping in spatial transcriptomics data. Recent spatial
        transcriptomics experiments utilize slides containing thousands
        of spots with spot-specific barcodes that bind mRNA. Ideally,
        unique molecular identifiers at a spot measure spot-specific
        expression, but this is often not the case due to bleed from
        nearby spots, an artifact we refer to as spot swapping.
        SpotClean is able to estimate the contamination rate in
        observed data and decontaminate the spot swapping effect, thus
        increase the sensitivity and precision of downstream analyses.
License: GPL-3
NeedsCompilation: yes
VignetteBuilder: knitr
Encoding: UTF-8
RoxygenNote: 7.3.3
URL: https://github.com/zijianni/SpotClean
BugReports: https://github.com/zijianni/SpotClean/issues
Language: en-US
Config/pak/sysreqs: libglpk-dev make libmagick++-dev gsfonts libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libxml2-dev libssl-dev
        python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-02-04 01:30:03 UTC
RemoteUrl: https://github.com/bioc/SpotClean
RemoteRef: RELEASE_3_22
RemoteSha: b674f0949565cc0a3c84e6f890cd2a4f0468095e
Packaged: 2026-03-06 09:12:17 UTC; root
Author: Zijian Ni [aut, cre] (ORCID: <https://orcid.org/0000-0003-1181-8337>),
  Christina Kendziorski [ctb]
Maintainer: Zijian Ni <zni25@wisc.edu>
Built: R 4.5.2; ; 2026-03-06 09:15:02 UTC; windows
