{
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  "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": "3.16.0",
  "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",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:51 UTC",
  "RemoteUrl": "https://github.com/bioc/GeomxTools",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "6033ab5ab6c128cd27face71a4eadd67444d1822",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-04 07:11:51 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>",
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    "analyte",
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    "as.SpatialExperiment",
    "checkQCFlags",
    "computeNormalizationFactors",
    "countsShiftedByOne",
    "design",
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    "dimLabels",
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    "featureType<-",
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    "iggNames",
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    "ngeoSD",
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    "plotConcordance",
    "plotNormFactorConcordance",
    "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": [
        "analyte",
        "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"
      ]
    },
    {
      "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"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/GeomxTools/raw/RELEASE_3_23/README.md",
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      "source": "GeomxSet_coercions.Rmd",
      "filename": "GeomxSet_coercions.html",
      "title": "Coercion of GeoMxSet to Seurat and SpatialExperiment Objects",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Data Processing",
        "Seurat",
        "Seurat Coercion",
        "Simple GeoMx data workflow",
        "In-depth GeoMx data workflow",
        "Spatial Graphing",
        "SpatialExperiment",
        "SpatialExperiment Coercion",
        "Image Overlays"
      ],
      "created": "2022-02-04 00:36:53",
      "modified": "2025-09-12 17:02:50",
      "commits": 11
    },
    {
      "source": "Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd",
      "filename": "Developer_Introduction_to_the_NanoStringGeoMxSet.html",
      "title": "Developer Introduction to the NanoStringGeoMxSet",
      "author": "David Henderson, Patrick Aboyoun, Nicole Ortogero, Zhi Yang, Jason Reeves, Kara Gorman, Rona Vitancol, Thomas Smith, Maddy Griswold",
      "engine": "knitr::rmarkdown",
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        "Loading Packages",
        "Building a NanoStringGeoMxSet from .DCC files",
        "How is the DSP data stored in the NanoStringGeoMxSet object?",
        "Accessing and Assigning NanoStringGeoMxSet Data Members",
        "Access annotations",
        "Summarizing NanoString GeoMx Data",
        "Subsetting NanoStringGeoMxSet Objects",
        "Apply Functions Across Assay Data",
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        "Normalization",
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      "title": "Protein data using GeomxTools",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Data Processing",
        "RNA",
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        "Segment QC",
        "Target QC",
        "Normalization"
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