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  "Title": "Background Normalisation for Multiplex Spatial Proteomics",
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  "Authors@R": "c(\nperson(\"Dharmesh D.\", \"Bhuva\", role = c(\"aut\", \"cre\"),\nemail = \"d.bhuva@uq.edu.au\",\ncomment = c(ORCID = \"0000-0002-6398-9157\")),\nperson(\"Rafael\", \"Tubelleza\", role = \"aut\",\nemail = \"r.tubelleza@uq.edu.au\",\ncomment = c(ORCID = \"0009-0007-1414-547X\")),\nperson(\"Malvika\", \"Kharbanda\", role = \"aut\",\nemail = \"malvika.kharbanda@adelaide.edu.au\",\ncomment = c(ORCID = \"0000-0001-9726-3023\")),\nperson(\"Agus\", \"Salim\", role = \"aut\",\nemail = \"salim.a@unimelb.edu.au\",\ncomment = c(ORCID = \"0000-0003-3999-7701\")))",
  "Description": "Implements bgnorm, a generative statistical framework for\nbackground correction, normalisation, and quality control in\nmultiplex spatial proteomics. The method models fluorescence\npixel intensities as a three-component mixture of log-normal\nconvolutions representing background, non-specific binding, and\nbiological signal. A deconvolution step separates the signal\ncomponent from background sources, and a model-based quantile\nnormalisation (bgnormQ) unifies measurements across markers,\nsamples, and three-dimensional tissue slices. A Jensen-Shannon\nDivergence metric provides automated quality control. A\nJava-free reader for Akoya PhenoCycler-Fusion QPTIFF, OME-TIFF,\nand OME-Zarr (OME-NGFF) images is included.",
  "License": "MIT + file LICENSE",
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      "title": "bgnormR: Background Normalisation for Multiplex Spatial Proteomics",
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        "bgnormR"
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      "title": "Subset a QPTIFFImage",
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        "as.QPTIFFImage.DelayedArray",
        "as.QPTIFFImage.QPTIFFImage"
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    {
      "page": "bgnorm_cells",
      "title": "Cell-level background normalisation (bgnorm)",
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    },
    {
      "page": "bgnorm_pixels",
      "title": "Pixel-level background normalisation (bgnorm) for a QPTIFFImage",
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    },
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      "title": "Per-channel bgnorm results stored in a QPTIFFImage",
      "topics": [
        "bgnorm_results"
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    },
    {
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      "title": "Apply cell-level bgnorm to a SingleCellExperiment or matrix",
      "topics": [
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    },
    {
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      "title": "BgnormResult S3 class",
      "topics": [
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    },
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      "topics": [
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      "topics": [
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      "page": "jsd_gaussians",
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      "topics": [
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    },
    {
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      "title": "Compute the JSD quality control metric from bgnorm model parameters",
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      "title": "Log2 transform with cofactor",
      "topics": [
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        "metadata.QPTIFFImage"
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        "dimnames,OMEZarrArraySeed-method",
        "extract_array,OMEZarrArraySeed-method",
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      "page": "QPTIFFMetadata",
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