{
  "_id": "6a494afdf6c47c4419498dfd",
  "Package": "GeomxTools",
  "Title": "NanoString GeoMx Tools",
  "Description": "Tools for NanoString Technologies GeoMx Technology.\nPackage provides functions for reading in DCC and PKC files\nbased on an ExpressionSet derived object.  Normalization and QC\nfunctions are also included.",
  "Version": "3.17.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(person(\"Maddy\", \"Griswold\", email = \"mgriswold@nanostring.com\", role = c(\"cre\", \"aut\")),\nperson(\"Nicole\", \"Ortogero\", email = \"nortogero@nanostring.com\", role = c(\"aut\")),\nperson(\"Zhi\", \"Yang\", role = c(\"aut\")),\nperson(\"Ronalyn\", \"Vitancol\", email = \"rvitancol@nanostring.com\", role = c(\"aut\")),\nperson(\"David\", \"Henderson\", role = c(\"aut\")))",
  "License": "MIT",
  "Collate": "DccMetadata.R NanoStringGeoMxSet-class.R\nNanoStringGeoMxSet-validity.R NanoStringGeoMxSet-accessors.R\nNanoStringGeoMxSet-qc.R NanoStringGeoMxSet-autoplot.R\nNanoStringGeoMxSet-aggregate.R NanoStringGeoMxSet-signatures.R\nNanoStringGeoMxSet-normalize.R NanoStringGeoMxSet-de.R\ncoercions.R readDccFile.R readPKCFile.R\nreadNanoStringGeoMxSet.R writeNanoStringGeoMxSet.R utils.R\noutliersFunctions.R",
  "biocViews": "GeneExpression, Transcription, CellBasedAssays, DataImport,\nTranscriptomics, Proteomics, mRNAMicroarray,\nProprietaryPlatforms, RNASeq, Sequencing, ExperimentalDesign,\nNormalization, Spatial",
  "VignetteEngine": "knitr::rmarkdown",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:51 UTC",
  "RemoteUrl": "https://github.com/bioc/GeomxTools",
  "RemoteRef": "HEAD",
  "RemoteSha": "37ea8120ca3d3d2649e810ec8cdfcd035fe95307",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-03 17:09:45 UTC",
    "User": "root"
  },
  "Author": "Maddy Griswold [cre, aut],\nNicole Ortogero [aut],\nZhi Yang [aut],\nRonalyn Vitancol [aut],\nDavid Henderson [aut]",
  "Maintainer": "Maddy Griswold <mgriswold@nanostring.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "GeomxTools_3.17.0.tar.gz",
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  "_created": "2026-07-03T17:09:45.000Z",
  "_published": "2026-07-04T18:03:40.892Z",
  "_bioccheck": {
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    "warning": 2,
    "note": 16
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  "_host": "GitHub-Actions",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "analyte",
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    "as.SpatialExperiment",
    "checkQCFlags",
    "computeNormalizationFactors",
    "countsShiftedByOne",
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    "iggNames",
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    "NanoStringGeoMxSet",
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    "ngeoSD",
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    "qcProteinSignal",
    "qcProteinSignalNames",
    "readDccFile",
    "readNanoStringGeoMxSet",
    "readPKCFile",
    "sData",
    "setBackgroundQCFlags",
    "setBioProbeQCFlags",
    "setGeoMxQCFlags",
    "setSegmentQCFlags",
    "setSeqQCFlags",
    "shiftCountsOne",
    "show",
    "signatureGroups",
    "signatures",
    "signatures<-",
    "signatureScores",
    "summarizeNegatives",
    "svarLabels",
    "updateGeoMxSet",
    "writeNanoStringGeoMxSet"
  ],
  "_help": [
    {
      "page": "aggregateCounts",
      "title": "Aggregate probe counts to target level for feature data",
      "topics": [
        "aggregateCounts"
      ]
    },
    {
      "page": "as.Seurat",
      "title": "Convert GeoMxSet Object to SeuratObject",
      "concept": [
        "objects"
      ],
      "topics": [
        "as.Seurat",
        "as.Seurat.NanoStringGeoMxSet"
      ]
    },
    {
      "page": "as.SpatialExperiment",
      "title": "Convert Object to SpatialExperiment",
      "topics": [
        "as.SpatialExperiment",
        "as.SpatialExperiment.NanoStringGeoMxSet"
      ]
    },
    {
      "page": "checkQCFlags",
      "title": "Check QC Flags in the GeoMxSet and removes the probe or sample from the object",
      "topics": [
        "checkQCFlags"
      ]
    },
    {
      "page": "checkQCFlags-NanoStringGeoMxSet-method",
      "title": "checkQCFlags",
      "topics": [
        "checkQCFlags,NanoStringGeoMxSet-method"
      ]
    },
    {
      "page": "compareToConfig",
      "title": "Compare given PKC probes to probes in config file",
      "topics": [
        "compareToConfig"
      ]
    },
    {
      "page": "computeNormalizationFactors",
      "title": "Generate normalization factors",
      "topics": [
        "computeNormalizationFactors"
      ]
    },
    {
      "page": "countsShiftedByOne",
      "title": "Accessor to check if \"exprs\" 'assDataElement' was shifted by one",
      "topics": [
        "countsShiftedByOne"
      ]
    },
    {
      "page": "hkNames",
      "title": "Return the House Keeper positive controls for protein",
      "topics": [
        "hkNames"
      ]
    },
    {
      "page": "iggNames",
      "title": "Return the IgG negative controls for protein",
      "topics": [
        "iggNames"
      ]
    },
    {
      "page": "logtBase",
      "title": "Get take the log of a numeric vector",
      "topics": [
        "logtBase"
      ]
    },
    {
      "page": "mixedModelDE",
      "title": "Run a mixed model on GeoMxSet",
      "topics": [
        "mixedModelDE"
      ]
    },
    {
      "page": "NanoStringGeoMxSet-class",
      "title": "Class to Contain NanoString Spatial Expression Level Assays",
      "topics": [
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        "analyte,NanoStringGeoMxSet-method",
        "class:NanoStringGeoMxSet",
        "coerce,ExpressionSet,NanoStringGeoMxSet-method",
        "design,NanoStringGeoMxSet-method",
        "design<-,NanoStringGeoMxSet,ANY-method",
        "design<-,NanoStringGeoMxSet,formula-method",
        "design<-,NanoStringGeoMxSet,NULL-method",
        "dimLabels,NanoStringGeoMxSet-method",
        "dimLabels<-,NanoStringGeoMxSet,character-method",
        "featureType",
        "featureType,NanoStringGeoMxSet-method",
        "featureType<-",
        "featureType<-,NanoStringGeoMxSet,character-method",
        "NanoStringGeoMxSet",
        "NanoStringGeoMxSet,environment-method",
        "NanoStringGeoMxSet,ExpressionSet-method",
        "NanoStringGeoMxSet,matrix-method",
        "NanoStringGeoMxSet,missing-method",
        "NanoStringGeoMxSet,NanoStringGeoMxSet-method",
        "NanoStringGeoMxSet-class",
        "sData",
        "sData,NanoStringGeoMxSet-method",
        "show,NanoStringGeoMxSet-method",
        "signatureGroups",
        "signatureGroups,NanoStringGeoMxSet-method",
        "signatures",
        "signatures,NanoStringGeoMxSet-method",
        "signatures<-",
        "signatures<-,NanoStringGeoMxSet,SignatureSet-method",
        "signatureScores",
        "signatureScores,NanoStringGeoMxSet-method",
        "svarLabels",
        "svarLabels,NanoStringGeoMxSet-method",
        "updateObject,NanoStringGeoMxSet-method"
      ]
    },
    {
      "page": "ngeoMean",
      "title": "Get the geometric mean of a vector",
      "topics": [
        "ngeoMean"
      ]
    },
    {
      "page": "ngeoSD",
      "title": "Get the geometric standard deviation of a vector",
      "topics": [
        "ngeoSD"
      ]
    },
    {
      "page": "normalize-NanoStringGeoMxSet-method",
      "title": "normalize",
      "topics": [
        "normalize,NanoStringGeoMxSet-method"
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    },
    {
      "page": "plotConcordance",
      "title": "Generate concordance figure of targets based on user provided factors",
      "topics": [
        "plotConcordance"
      ]
    },
    {
      "page": "plotNormFactorConcordance",
      "title": "Generate concordance figure of normalization factors based on user provided factors",
      "topics": [
        "plotNormFactorConcordance"
      ]
    },
    {
      "page": "qcProteinSignal",
      "title": "Generate Protein QC signal boxplot figure",
      "topics": [
        "qcProteinSignal"
      ]
    },
    {
      "page": "qcProteinSignalNames",
      "title": "Generate list of proteins ordered by SNR",
      "topics": [
        "qcProteinSignalNames"
      ]
    },
    {
      "page": "readDccFile",
      "title": "Read DCC File",
      "topics": [
        "readDccFile"
      ]
    },
    {
      "page": "readNanoStringGeoMxSet",
      "title": "Read 'NanoStringGeoMxSet'",
      "concept": [
        "NanoStringGeoMxSet"
      ],
      "topics": [
        "readNanoStringGeoMxSet"
      ]
    },
    {
      "page": "readPKCFile",
      "title": "Read PKC File",
      "topics": [
        "readPKCFile"
      ]
    },
    {
      "page": "setBackgroundQCFlags",
      "title": "Add background QC flags to NanoStringGeoMxSet object protocol data",
      "topics": [
        "setBackgroundQCFlags"
      ]
    },
    {
      "page": "setBioProbeQCFlags",
      "title": "Add probe QC flags to NanoStringGeoMxSet object feature data",
      "topics": [
        "setBioProbeQCFlags"
      ]
    },
    {
      "page": "setGeoMxQCFlags",
      "title": "Add GeoMx segment QC flags to NanoStringGeoMxSet object protocol data",
      "topics": [
        "setGeoMxQCFlags"
      ]
    },
    {
      "page": "setQCFlags-NanoStringGeoMxSet-method",
      "title": "Add QC flags to feature and protocol data simultaneously",
      "topics": [
        "setQCFlags,NanoStringGeoMxSet-method"
      ]
    },
    {
      "page": "setSegmentQCFlags",
      "title": "Add segment QC flags to protocol data",
      "topics": [
        "setSegmentQCFlags"
      ]
    },
    {
      "page": "setSeqQCFlags",
      "title": "Add sequencing QC flags to NanoStringGeoMxSet object protocol data",
      "topics": [
        "setSeqQCFlags"
      ]
    },
    {
      "page": "shiftCountsOne",
      "title": "Add one to all counts in an expression matrix",
      "topics": [
        "shiftCountsOne"
      ]
    },
    {
      "page": "summarizeNegatives",
      "title": "Calculate negative probe summary stats",
      "topics": [
        "summarizeNegatives"
      ]
    },
    {
      "page": "updateGeoMxSet",
      "title": "Update GeoMxSet object to current version",
      "topics": [
        "updateGeoMxSet"
      ]
    },
    {
      "page": "writeNanoStringGeoMxSet",
      "title": "write 'NanoStringGeoMxSet'",
      "concept": [
        "NanoStringGeoMxSet"
      ],
      "topics": [
        "writeNanoStringGeoMxSet"
      ]
    }
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