{
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  "Package": "immunoClust",
  "Type": "Package",
  "Title": "immunoClust - Automated Pipeline for Population Detection in\nFlow Cytometry",
  "Version": "1.44.0",
  "Date": "2025-09-18",
  "Authors@R": "person(\"Till\", \"Soerensen\", email=\"till.soerensen@bioretis.com\",\nrole=c(\"aut\", \"cre\"))",
  "Maintainer": "Till Soerensen <till.soerensen@bioretis.com>",
  "Description": "immunoClust is a model based clustering approach for Flow\nCytometry samples. The cell-events of single Flow Cytometry\nsamples are modelled by a mixture of multinominal normal- or\nt-distributions. The cell-event clusters of several samples are\nmodelled by a mixture of multinominal normal-distributions\naiming stable co-clusters across these samples.",
  "Collate": "generics.R class.immunoClust.R plot.immunoClust.R\nsplom.immunoClust.R methods.immunoClust.R class.immunoMeta.R\nplot.immunoMeta.R methods.immunoMeta.R data.R process.R\ncell.clustering.R meta.clustering.R meta.annotation.R\nmeta.SON.R meta.export.R clust.util.R transform.R",
  "biocViews": "Clustering, FlowCytometry, SingleCell, CellBasedAssays,\nImmunoOncology",
  "License": "Artistic-2.0",
  "Config/pak/sysreqs": "libssl-dev",
  "Repository": "Bioconductor 3.23",
  "Date/Publication": "2026-04-28 12:40:46 UTC",
  "RemoteUrl": "https://github.com/bioc/immunoClust",
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  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-14 09:43:20 UTC",
    "User": "root"
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  "Author": "Till Soerensen [aut, cre]",
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  "_created": "2026-10-14T09:43:20.000Z",
  "_published": "2026-10-14T10:18:24.067Z",
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  "_upstream": "https://github.com/bioc/immunoClust",
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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 even y prior to creation of RELEASE_3_23 branch\n",
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  "_topics": [
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    "flowcytometry",
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    "cellbasedassays",
    "immunooncology",
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  "_exports": [
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    "aposteriori",
    "bhattacharyya.coeff",
    "bhattacharyya.dist",
    "bhattacharyya.prob",
    "cell.Classify",
    "cell.classifyAll",
    "cell.ClustData",
    "cell.EMstep",
    "cell.EMt",
    "cell.Estep",
    "cell.FitModel",
    "cell.hclust",
    "cell.InitialModel",
    "cell.MajorIterationLoop",
    "cell.MajorIterationTrans",
    "cell.MEstep",
    "cell.Mstep",
    "cell.process",
    "cell.SubClustering",
    "cell.TestSubCluster",
    "cells",
    "classified",
    "clusterCoeff",
    "clusterDist",
    "clusterProb",
    "clusters",
    "desc",
    "desc<-",
    "descFull",
    "events",
    "finalize",
    "findLevel",
    "immunoMeta",
    "label",
    "level",
    "level<-",
    "meta.Clustering",
    "meta.exprs",
    "meta.freqTable",
    "meta.hclust",
    "meta.ME",
    "meta.Normalize",
    "meta.numClusters",
    "meta.numEvents",
    "meta.parMFI",
    "meta.process",
    "meta.RegNorm",
    "meta.relEvents",
    "meta.relParent",
    "meta.SON.clustering",
    "meta.SON.combineClustering",
    "meta.SubClustering",
    "meta.TestSubCluster",
    "move<-",
    "mu",
    "ncls",
    "nobs",
    "npar",
    "nsam",
    "parameters",
    "parent<-",
    "plot",
    "prop",
    "prop<-",
    "remove<-",
    "removed.above",
    "removed.below",
    "sam_clsEvents",
    "sam_clsMu",
    "sam_clsSigma",
    "sam_clsWeights",
    "sam_names",
    "sam_ncls",
    "show",
    "sigma",
    "splom",
    "subset",
    "summary",
    "trans.ApplyToData",
    "trans.FitToData",
    "transfer<-",
    "transformParams",
    "unclassified",
    "weights"
  ],
  "_datasets": [
    {
      "name": "dat.exp",
      "title": "immunoClust Meta-clustering Sample",
      "object": "dat.exp",
      "file": "dat.exp.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dat.fcs",
      "title": "immunoClust Cell-clustering Sample",
      "object": "dat.fcs",
      "file": "dat.fcs.RData",
      "class": [
        "flowFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dat.meta",
      "title": "immunoClust Meta-clustering Results Sample",
      "object": "dat.meta",
      "file": "dat.meta.RData",
      "class": [
        "immunoMeta"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "immunoClust-package",
      "title": "immunoClust - Automated Pipeline for Population Detection in Flow Cytometry",
      "topics": [
        "immunoClust-package",
        "immunoClust",
        "immunoClust.package"
      ]
    },
    {
      "page": "bhattacharyya",
      "title": "Bhattacharyya Distance, Coefficient and Probability",
      "topics": [
        "bhattacharyya.coeff",
        "bhattacharyya.dist",
        "bhattacharyya.prob"
      ]
    },
    {
      "page": "cell.ClustData",
      "title": "Model Based Clustering of Data for a pre-defined Number of Clusters",
      "topics": [
        "cell.ClustData"
      ]
    },
    {
      "page": "cell.EM",
      "title": "immunoClust EMt-iteration on Cell-events given initial Model Parameters",
      "topics": [
        "cell.EMstep",
        "cell.EMt",
        "cell.Estep"
      ]
    },
    {
      "page": "cell.FitModel",
      "title": "immunoClust EMt-iteration on Cell-events given initial Model Parameters",
      "topics": [
        "cell.Classify",
        "cell.FitModel"
      ]
    },
    {
      "page": "cell.hclust",
      "title": "Hierarchical Model Based Clustering of Cell-events in the immunoClust-pipeline",
      "topics": [
        "cell.hclust"
      ]
    },
    {
      "page": "cell.ME",
      "title": "immunoClust EM-iteration on Cell-events given initial Cluster Membership Assignment",
      "topics": [
        "cell.MEstep",
        "cell.Mstep"
      ]
    },
    {
      "page": "cell.process",
      "title": "Clustering of Cell-events in the immunoClust-pipeline",
      "topics": [
        "cell.classifyAll",
        "cell.InitialModel",
        "cell.MajorIterationLoop",
        "cell.MajorIterationTrans",
        "cell.process"
      ]
    },
    {
      "page": "cell.removed",
      "title": "Brief Information of removed Cell-events by immunoClust Cell-event Clustering",
      "topics": [
        "removed.above",
        "removed.below"
      ]
    },
    {
      "page": "cell.SubClustering",
      "title": "immunoClust Model Refinement Step in iterative Cell-events Clustering",
      "topics": [
        "cell.SubClustering",
        "cell.TestSubCluster"
      ]
    },
    {
      "page": "dat.exp",
      "title": "immunoClust Meta-clustering Sample",
      "topics": [
        "dat.exp"
      ]
    },
    {
      "page": "dat.fcs",
      "title": "immunoClust Cell-clustering Sample",
      "topics": [
        "dat.fcs"
      ]
    },
    {
      "page": "dat.meta",
      "title": "immunoClust Meta-clustering Results Sample",
      "topics": [
        "dat.meta"
      ]
    },
    {
      "page": "generics",
      "title": "Generic function definitions in immunoClust",
      "topics": [
        "aposteriori",
        "clusterCoeff",
        "clusterDist",
        "clusterProb",
        "label",
        "mu",
        "ncls",
        "nobs",
        "npar",
        "nsam",
        "parameters",
        "parameters<-",
        "sam_clsEvents",
        "sam_clsMu",
        "sam_clsSigma",
        "sam_clsWeights",
        "sam_names",
        "sam_ncls",
        "sigma",
        "subset",
        "transformParams",
        "weights"
      ]
    },
    {
      "page": "immunoClust.object",
      "title": "immunoClust-Object",
      "topics": [
        "immunoClust-class",
        "immunoClust.object",
        "show",
        "show,immunoClust-method",
        "show.immunoClust",
        "summary",
        "summary,immunoClust-method",
        "summary.immunoClust"
      ]
    },
    {
      "page": "immunoMeta.object",
      "title": "'immunoMeta': a class for storing meta-clustering results",
      "topics": [
        "immunoMeta",
        "immunoMeta-class",
        "immunoMeta-object",
        "immunoMeta.class",
        "immunoMeta.object",
        "show,immunoMeta-method",
        "show.immunoMeta",
        "summary,immunoMeta-method",
        "summary.immunoMeta"
      ]
    },
    {
      "page": "meta.clustering",
      "title": "Clustering of Cell-clusters in the immunoClust-pipeline",
      "topics": [
        "meta.Clustering"
      ]
    },
    {
      "page": "meta.export",
      "title": "immunoClust Meta-clustering Results Export",
      "topics": [
        "meta.export",
        "meta.freqTable",
        "meta.majorEvents",
        "meta.numClusters",
        "meta.numEvents",
        "meta.parMFI",
        "meta.relEvents",
        "meta.relEvents2",
        "meta.relEvents3",
        "meta.relParent"
      ]
    },
    {
      "page": "meta.exprs",
      "title": "Collecting Data of an immunoClust vector",
      "topics": [
        "meta.exprs"
      ]
    },
    {
      "page": "meta.hclust",
      "title": "Hierarchical Meta-clustering of Cell-clusters in the immunoClust-pipeline",
      "topics": [
        "meta.hclust"
      ]
    },
    {
      "page": "meta.ME",
      "title": "immunoClust EM(t)-iteration on Cell-clusters",
      "topics": [
        "meta.ME"
      ]
    },
    {
      "page": "meta.normalize",
      "title": "immunoClust normalization step with the meta.clustering process",
      "topics": [
        "meta.Normalize"
      ]
    },
    {
      "page": "meta.process",
      "title": "Meta-clustering of Cell-clusters in the immunoClust-pipeline",
      "topics": [
        "meta.process"
      ]
    },
    {
      "page": "meta.regnorm",
      "title": "immunoClust normalization procedure",
      "topics": [
        "meta.RegNorm"
      ]
    },
    {
      "page": "SON.clustering",
      "title": "meta clustering process with internal SON normalisation",
      "topics": [
        "meta.SON.clustering"
      ]
    },
    {
      "page": "SON.combineClustering",
      "title": "Transfer the annotation of an immunoMeta-object to an immunoClust-object.",
      "topics": [
        "meta.SON.combineClustering"
      ]
    },
    {
      "page": "meta.SubClustering",
      "title": "immunoClust Model Refinement Step in iterative Meta-clustering",
      "topics": [
        "meta.SubClustering",
        "meta.TestSubCluster"
      ]
    },
    {
      "page": "immunoClust.methods",
      "title": "Acessors and Methods for immunoClust Objects",
      "topics": [
        "aposteriori,immunoClust-method",
        "aposteriori.immunoClust",
        "cells",
        "cells,immunoClust-method",
        "events,immunoClust-method",
        "events.immunoClust",
        "label,immunoClust-method",
        "label.immunoClust",
        "mu,immunoClust-method",
        "mu.immunoClust",
        "ncls,immunoClust-method",
        "ncls.immunoClust",
        "nobs,immunoClust-method",
        "nobs.immunoClust",
        "npar,immunoClust-method",
        "npar.immunoClust",
        "parameters,immunoClust-method",
        "parameters.immunoClust",
        "parameters<-,immunoClust,character-method",
        "parameters<-.immunoClust",
        "sigma,immunoClust-method",
        "sigma.immunoClust",
        "subset,immunoClust-method",
        "subset.immunoClust",
        "transformParams,immunoClust-method",
        "transformParams.immunoClust",
        "weights,immunoClust-method",
        "weights.immunoClust"
      ]
    },
    {
      "page": "immunoMeta.methods",
      "title": "Acessors and Methods for immunoMeta Objects",
      "topics": [
        "addLevel<-",
        "addLevel<-.immunoMeta",
        "aposteriori,immunoMeta-method",
        "aposteriori.immunoMeta",
        "classified",
        "classified,immunoMeta-method",
        "classified.immunoMeta",
        "clusterCoeff,immunoMeta-method",
        "clusterDist,immunoMeta-method",
        "clusterProb,immunoMeta-method",
        "clusters",
        "clusters,immunoMeta-method",
        "clusters.immunoMeta",
        "desc",
        "desc,immunoMeta-method",
        "desc.immunoMeta",
        "desc<-",
        "desc<-,immunoMeta-method",
        "desc<-.immunoMeta",
        "descFull",
        "descFull,immunoMeta-method",
        "descFull.immunoMeta",
        "events",
        "events,immunoMeta-method",
        "events.immunoMeta",
        "finalize",
        "finalize,immunoMeta-method",
        "finalize.immunoMeta",
        "findLevel",
        "findLevel,immunoMeta-method",
        "findLevel.immunoMeta",
        "label,immunoMeta-method",
        "label.immunoMeta",
        "level",
        "level,immunoMeta-method",
        "level.immunoMeta",
        "level<-",
        "level<-.immunoMeta",
        "move<-",
        "move<-.immunoMeta",
        "mu,immunoMeta-method",
        "mu.immunoMeta",
        "ncls,immunoMeta-method",
        "ncls.immunoMeta",
        "nobs,immunoMeta-method",
        "nobs.immunoMeta",
        "npar,immunoMeta-method",
        "npar.immunoMeta",
        "nsam,immunoMeta-method",
        "nsam.immunoMeta",
        "parameters,immunoMeta-method",
        "parameters.immunoMeta",
        "parameters<-,immunoMeta,character-method",
        "parameters<-.immunoMeta",
        "parent<-",
        "parent<-.immunoMeta",
        "parent<-.immunoMeta-method",
        "prop",
        "prop,immunoMeta-method",
        "prop.immunoMeta",
        "prop<-",
        "prop<-,immunoMeta-method",
        "prop<-.immunoMeta",
        "remove<-",
        "remove<-.immunoMeta",
        "sam_clsEvents,immunoMeta-method",
        "sam_clsEvents.immunoMeta",
        "sam_clsMu,immunoMeta-method",
        "sam_clsMu.immunoMeta",
        "sam_clsSigma,immunoMeta-method",
        "sam_clsSigma.immunoMeta",
        "sam_clsWeights,immunoMeta-method",
        "sam_clsWeights.immunoMeta",
        "sam_names,immunoMeta-method",
        "sam_names.immunoMeta",
        "sam_ncls,immunoMeta-method",
        "sam_ncls.immunoMeta",
        "sigma,immunoMeta-method",
        "sigma.immunoMeta",
        "subset,immunoMeta-method",
        "subset.immunoMeta",
        "transfer<-",
        "transfer<-,immunoMeta,immunoMeta-method",
        "transfer<-.immunoMeta",
        "transformParams,immunoMeta-method",
        "transformParams.immunoMeta",
        "unclassified",
        "unclassified,immunoMeta-method",
        "unclassified.immunoMeta",
        "weights,immunoMeta-method",
        "weights.immunoMeta"
      ]
    },
    {
      "page": "plot.immunoClust",
      "title": "Scatterplot of immunoClust Clustering Results",
      "topics": [
        "plot,immunoClust,missing-method",
        "plot,immunoClust-method",
        "plot.immunoClust"
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