Package: bgnormR
Type: Package
Title: Background Normalisation for Multiplex Spatial Proteomics
Version: 0.99.5
Authors@R: c(
    person("Dharmesh D.", "Bhuva", role = c("aut", "cre"),
           email = "d.bhuva@uq.edu.au",
           comment = c(ORCID = "0000-0002-6398-9157")),
    person("Rafael", "Tubelleza", role = "aut",
           email = "r.tubelleza@uq.edu.au",
           comment = c(ORCID = "0009-0007-1414-547X")),
    person("Malvika", "Kharbanda", role = "aut",
           email = "malvika.kharbanda@adelaide.edu.au",
           comment = c(ORCID = "0000-0001-9726-3023")),
    person("Agus", "Salim", role = "aut",
           email = "salim.a@unimelb.edu.au",
           comment = c(ORCID = "0000-0003-3999-7701")))
Description: Implements bgnorm, a generative statistical framework for
        background correction, normalisation, and quality control in
        multiplex spatial proteomics. The method models fluorescence
        pixel intensities as a three-component mixture of log-normal
        convolutions representing background, non-specific binding, and
        biological signal. A deconvolution step separates the signal
        component from background sources, and a model-based quantile
        normalisation (bgnormQ) unifies measurements across markers,
        samples, and three-dimensional tissue slices. A Jensen-Shannon
        Divergence metric provides automated quality control. A
        Java-free reader for Akoya PhenoCycler-Fusion QPTIFF, OME-TIFF,
        and OME-Zarr (OME-NGFF) images is included.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: mclust (>= 5.4), SummarizedExperiment (>= 1.28.0),
        SpatialExperiment (>= 1.10.0), BiocParallel (>= 1.30.0),
        DelayedArray (>= 0.26.0), S4Vectors, ggplot2 (>= 3.4.0),
        scales, stats, utils, methods
Suggests: SingleCellExperiment (>= 1.20.0), scattermore, tiff (>=
        0.1-11), xml2 (>= 1.3), jsonlite, ijtiff, Rarr, BiocStyle,
        knitr, rmarkdown, testthat (>= 3.0.0), EBImage
VignetteBuilder: knitr
biocViews: Normalization, Preprocessing, SingleCell, Spatial,
        Proteomics, ImmunoOncology, QualityControl, DataImport
Config/testthat/edition: 3
URL: https://github.com/BhuvaLab/bgnormR
BugReports: https://github.com/BhuvaLab/bgnormR/issues
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libmagick++-dev gsfonts libicu-dev libssl-dev
        zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-11-08 11:09:56 UTC
RemoteUrl: https://github.com/BiocStaging/bgnormR
RemoteRef: HEAD
RemoteSha: b187a5be699d2bb126555d0af1734c6852d6adf4
NeedsCompilation: no
Packaged: 2026-11-10 01:56:38 UTC; root
Author: Dharmesh D. Bhuva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6398-9157>),
  Rafael Tubelleza [aut] (ORCID: <https://orcid.org/0009-0007-1414-547X>),
  Malvika Kharbanda [aut] (ORCID:
    <https://orcid.org/0000-0001-9726-3023>),
  Agus Salim [aut] (ORCID: <https://orcid.org/0000-0003-3999-7701>)
Maintainer: Dharmesh D. Bhuva <d.bhuva@uq.edu.au>