{
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  "Package": "cummeRbund",
  "Title": "Analysis, exploration, manipulation, and visualization of\nCufflinks high-throughput sequencing data.",
  "Version": "2.54.0",
  "Date": "2013-04-22",
  "Author": "L. Goff, C. Trapnell, D. Kelley",
  "Description": "Allows for persistent storage, access, exploration, and\nmanipulation of Cufflinks high-throughput sequencing data.  In\naddition, provides numerous plotting functions for commonly\nused visualizations.",
  "Maintainer": "Loyal A. Goff <lgoff@csail.mit.edu>",
  "License": "Artistic-2.0",
  "Collate": "AllGenerics.R AllClasses.R database-setup.R methods-CuffSet.R\nmethods-CuffData.R methods-CuffDist.R methods-CuffGeneSet.R\nmethods-CuffFeatureSet.R methods-CuffGene.R\nmethods-CuffFeature.R tools.R zzz.R",
  "LazyLoad": "yes",
  "biocViews": "HighThroughputSequencing, HighThroughputSequencingData,\nRNAseq, RNAseqData, GeneExpression, DifferentialExpression,\nInfrastructure, DataImport, DataRepresentation, Visualization,\nBioinformatics, Clustering, MultipleComparisons, QualityControl",
  "PackageStatus": "Deprecated",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:35:54 UTC",
  "RemoteUrl": "https://github.com/bioc/cummeRbund",
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    "User": "root"
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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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  "_tags": [],
  "_topics": [
    "highthroughputsequencing",
    "highthroughputsequencingdata",
    "rnaseq",
    "rnaseqdata",
    "geneexpression",
    "differentialexpression",
    "infrastructure",
    "dataimport",
    "datarepresentation",
    "visualization",
    "bioinformatics",
    "clustering",
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    "qualitycontrol"
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_exports": [
    "addFeatures",
    "annotation",
    "CDS",
    "conditions",
    "count",
    "countMatrix",
    "csBoxplot",
    "csCluster",
    "csClusterPlot",
    "csDendro",
    "csDensity",
    "csDistHeat",
    "csFoldChangeHeatmap",
    "csHeatmap",
    "csNMF",
    "csPie",
    "csScatter",
    "csScatterMatrix",
    "csSpecificity",
    "csVolcano",
    "csVolcanoMatrix",
    "DB",
    "diffData",
    "diffTable",
    "dispersionPlot",
    "distValues",
    "expressionBarplot",
    "expressionPlot",
    "featureNames",
    "features",
    "findGene",
    "findSimilar",
    "fpkm",
    "fpkmMatrix",
    "fpkmSCVPlot",
    "genePlot",
    "genes",
    "getFeatures",
    "getGene",
    "getGeneId",
    "getGenes",
    "getLevels",
    "getRepLevels",
    "getSig",
    "getSigTable",
    "isoforms",
    "JSdist",
    "JSdistFromP",
    "JSdistVec",
    "makeGeneRegionTrack",
    "makeprobs",
    "makeprobsvec",
    "makeRnk",
    "MAplot",
    "MDSplot",
    "PCAplot",
    "promoters",
    "readCufflinks",
    "relCDS",
    "repCountMatrix",
    "repFpkm",
    "repFpkmMatrix",
    "replicates",
    "runInfo",
    "samples",
    "shannon.entropy",
    "sigMatrix",
    "splicing",
    "TSS",
    "varModel"
  ],
  "_datasets": [
    {
      "name": "PINK1",
      "title": "PINK1",
      "object": "sampleData",
      "file": "sampleData.rda",
      "class": [
        "CuffGene"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sampleGeneSet",
      "title": "sampleGeneSet",
      "object": "sampleData",
      "file": "sampleData.rda",
      "class": [
        "CuffGeneSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sampleIDs",
      "title": "sampleIDs",
      "object": "sampleData",
      "file": "sampleData.rda",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cummeRbund-package",
      "title": "cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~",
      "topics": [
        "cummeRbund-package",
        "cummeRbund"
      ]
    },
    {
      "page": "addFeatures",
      "title": "addFeatures",
      "topics": [
        "addFeatures",
        "addFeatures,CuffData-method",
        "addFeatures,CuffSet-method"
      ]
    },
    {
      "page": "count",
      "title": "Retrieve count values (raw and normalized)",
      "topics": [
        "count",
        "count,CuffData-method",
        "count,CuffFeature-method",
        "count,CuffFeatureSet-method",
        "count-methods"
      ]
    },
    {
      "page": "countMatrix",
      "title": "countMatrix",
      "topics": [
        "countMatrix",
        "countMatrix,CuffData-method",
        "countMatrix,CuffFeatureSet-method",
        "repCountMatrix",
        "repCountMatrix,CuffData-method",
        "repCountMatrix,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csBoxplot",
      "title": "csBoxplot",
      "topics": [
        "csBoxplot",
        "csBoxplot,CuffData-method"
      ]
    },
    {
      "page": "csCluster",
      "title": "csCluster",
      "topics": [
        "csCluster",
        "csCluster,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csClusterPlot",
      "title": "csClusterPlot",
      "topics": [
        "csClusterPlot"
      ]
    },
    {
      "page": "csDendro",
      "title": "csDendro",
      "topics": [
        "csDendro",
        "csDendro,CuffData-method",
        "csDendro,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csDensity",
      "title": "Density plot of CuffData",
      "topics": [
        "csDensity",
        "csDensity,CuffData-method",
        "csDensity,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csDistHeat",
      "title": "csDistHeat",
      "topics": [
        "csDistHeat",
        "csDistHeat,CuffData-method",
        "csDistHeat,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csHeatmap",
      "title": "csHeatmap",
      "topics": [
        "csFoldChangeHeatmap",
        "csFoldChangeHeatmap,CuffFeatureSet-method",
        "csHeatmap",
        "csHeatmap,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csScatter",
      "title": "Scatter Plot",
      "topics": [
        "csScatter",
        "csScatter,CuffData-method",
        "csScatter,CuffFeatureSet-method",
        "csScatterMatrix",
        "csScatterMatrix,CuffData-method"
      ]
    },
    {
      "page": "csSpecificity",
      "title": "csSpecificity",
      "topics": [
        "csSpecificity",
        "csSpecificity,CuffData-method",
        "csSpecificity,CuffFeatureSet-method"
      ]
    },
    {
      "page": "csVolcano",
      "title": "Volcano Plot",
      "topics": [
        "csVolcano",
        "csVolcano,CuffData-method",
        "csVolcano,CuffFeatureSet-method",
        "csVolcanoMatrix",
        "csVolcanoMatrix,CuffData-method"
      ]
    },
    {
      "page": "CuffData-class",
      "title": "Class \"CuffData\"",
      "topics": [
        "annotation,CuffData-method",
        "CuffData-class",
        "DB,CuffData-method",
        "dim,CuffData-method",
        "getFeatures,CuffData-method",
        "makeRnk",
        "makeRnk,CuffData-method"
      ]
    },
    {
      "page": "CuffDist-class",
      "title": "Class \"CuffDist\"",
      "topics": [
        "CuffDist-class",
        "DB,CuffDist-method",
        "dim,CuffDist-method",
        "samples,CuffDist-method"
      ]
    },
    {
      "page": "CuffFeature-class",
      "title": "Class \"CuffFeature\"",
      "topics": [
        "annotation,CuffFeature-method",
        "CuffFeature-class",
        "diffData,CuffFeature-method",
        "fpkmMatrix,CuffFeature-method",
        "length,CuffFeature-method",
        "samples,CuffFeature-method"
      ]
    },
    {
      "page": "CuffFeatureSet-class",
      "title": "Class \"CuffFeatureSet\"",
      "topics": [
        "annotation",
        "annotation,CuffFeatureSet-method",
        "CuffFeatureSet-class",
        "diffData,CuffFeatureSet-method",
        "featureNames,CuffFeatureSet-method",
        "features,CuffFeatureSet-method",
        "length,CuffFeatureSet-method",
        "samples,CuffFeatureSet-method"
      ]
    },
    {
      "page": "CuffGene-class",
      "title": "Class \"CuffGene\"",
      "topics": [
        "CDS,CuffGene-method",
        "csPie",
        "csPie,CuffGene-method",
        "CuffGene-class",
        "genePlot",
        "genePlot,CuffGene-method",
        "genes,CuffGene-method",
        "isoforms,CuffGene-method",
        "length,CuffGene-method",
        "makeGeneRegionTrack",
        "makeGeneRegionTrack,CuffGene-method",
        "promoters,CuffGene-method",
        "relCDS,CuffGene-method",
        "splicing,CuffGene-method",
        "TSS,CuffGene-method"
      ]
    },
    {
      "page": "CuffGeneSet-class",
      "title": "Class \"CuffGeneSet\"",
      "topics": [
        "CDS,CuffGeneSet-method",
        "CuffGeneSet-class",
        "genes,CuffGeneSet-method",
        "isoforms,CuffGeneSet-method",
        "promoters,CuffGeneSet-method",
        "relCDS,CuffGeneSet-method",
        "splicing,CuffGeneSet-method",
        "TSS,CuffGeneSet-method"
      ]
    },
    {
      "page": "CuffSet-class",
      "title": "Class \"CuffSet\"",
      "topics": [
        "CDS",
        "CDS,CuffSet-method",
        "conditions",
        "conditions,CuffSet-method",
        "CuffSet-class",
        "DB",
        "DB,CuffSet-method",
        "genes",
        "genes,CuffSet-method",
        "isoforms",
        "isoforms,CuffSet-method",
        "promoters",
        "promoters,CuffSet-method",
        "relCDS",
        "relCDS,CuffSet-method",
        "splicing",
        "splicing,CuffSet-method",
        "TSS",
        "TSS,CuffSet-method",
        "varModel",
        "varModel,CuffSet-method",
        "[,CuffSet-method"
      ]
    },
    {
      "page": "diffData",
      "title": "Differential comparison data",
      "topics": [
        "diffData",
        "diffData,CuffData-method",
        "diffTable",
        "diffTable,CuffData-method",
        "diffTable,CuffFeatureSet-method"
      ]
    },
    {
      "page": "dimensionality",
      "title": "Dimensionality reduction utilities",
      "topics": [
        "MDSplot",
        "MDSplot,CuffData-method",
        "MDSplot,CuffFeatureSet-method",
        "PCAplot",
        "PCAplot,CuffData-method",
        "PCAplot,CuffFeatureSet-method"
      ]
    },
    {
      "page": "dispersionPlot",
      "title": "Mean count vs dispersion plot",
      "topics": [
        "dispersionPlot",
        "dispersionPlot,CuffData-method",
        "dispersionPlot,CuffSet-method"
      ]
    },
    {
      "page": "distValues",
      "title": "distValues",
      "topics": [
        "distValues",
        "distValues,CuffDist-method"
      ]
    },
    {
      "page": "exploratory",
      "title": "Methods for Exploratory Analysis in cummeRbund",
      "topics": [
        "csNMF",
        "csNMF,CuffData-method",
        "csNMF,CuffFeatureSet-method"
      ]
    },
    {
      "page": "expressionBarplot",
      "title": "Barplot",
      "topics": [
        "expressionBarplot",
        "expressionBarplot,CuffFeature-method",
        "expressionBarplot,CuffFeatureSet-method"
      ]
    },
    {
      "page": "expressionPlot",
      "title": "Expression Plot",
      "topics": [
        "expressionPlot",
        "expressionPlot,CuffFeature-method",
        "expressionPlot,CuffFeatureSet-method"
      ]
    },
    {
      "page": "featureNames",
      "title": "Feature names",
      "topics": [
        "featureNames,CuffData-method"
      ]
    },
    {
      "page": "features",
      "title": "Features",
      "topics": [
        "features",
        "features,CuffGene-method"
      ]
    },
    {
      "page": "findGene",
      "title": "findGene",
      "topics": [
        "findGene",
        "findGene,CuffSet-method"
      ]
    },
    {
      "page": "findSimilar",
      "title": "findSimilar",
      "topics": [
        "findSimilar",
        "findSimilar,CuffSet-method"
      ]
    },
    {
      "page": "fpkm",
      "title": "Retrieve FPKM values",
      "topics": [
        "fpkm",
        "fpkm,CuffData-method",
        "fpkm,CuffFeature-method",
        "fpkm,CuffFeatureSet-method",
        "fpkm-methods"
      ]
    },
    {
      "page": "fpkmMatrix",
      "title": "fpkmMatrix",
      "topics": [
        "fpkmMatrix",
        "fpkmMatrix,CuffData-method",
        "fpkmMatrix,CuffFeatureSet-method",
        "repFpkmMatrix",
        "repFpkmMatrix,CuffData-method",
        "repFpkmMatrix,CuffFeature-method",
        "repFpkmMatrix,CuffFeatureSet-method"
      ]
    },
    {
      "page": "getFeatures",
      "title": "getFeatures",
      "topics": [
        "getFeatures",
        "getFeatures,CuffSet-method"
      ]
    },
    {
      "page": "getGene",
      "title": "getGene",
      "topics": [
        "getGene",
        "getGene,CuffSet-method"
      ]
    },
    {
      "page": "getGeneId",
      "title": "getGene",
      "topics": [
        "getGeneId",
        "getGeneId,CuffSet-method"
      ]
    },
    {
      "page": "getGenes",
      "title": "getGenes",
      "topics": [
        "getGenes",
        "getGenes,CuffSet-method"
      ]
    },
    {
      "page": "getLevels",
      "title": "getLevels",
      "topics": [
        "getLevels",
        "getLevels,CuffData-method",
        "getLevels,CuffSet-method"
      ]
    },
    {
      "page": "getRepLevels",
      "title": "getRepLevels",
      "topics": [
        "getRepLevels",
        "getRepLevels,CuffData-method",
        "getRepLevels,CuffSet-method"
      ]
    },
    {
      "page": "getSig",
      "title": "getSig",
      "topics": [
        "getSig",
        "getSig,CuffSet-method"
      ]
    },
    {
      "page": "getSigTable",
      "title": "getSigTable",
      "topics": [
        "getSigTable",
        "getSigTable,CuffSet-method"
      ]
    },
    {
      "page": "JSdist",
      "title": "Jensen-Shannon distance on columns",
      "topics": [
        "JSdist"
      ]
    },
    {
      "page": "JSdistFromP",
      "title": "Jensen-Shannon distance on rows from a pre-defined vector of probabilities",
      "topics": [
        "JSdistFromP"
      ]
    },
    {
      "page": "JSdistVec",
      "title": "JSdistVec",
      "topics": [
        "JSdistVec"
      ]
    },
    {
      "page": "makeprobs",
      "title": "Transform a matrix into probabilities by columns",
      "topics": [
        "makeprobs"
      ]
    },
    {
      "page": "makeprobsvec",
      "title": "makeprobsvec",
      "topics": [
        "makeprobsvec"
      ]
    },
    {
      "page": "MAplot",
      "title": "MAplot",
      "topics": [
        "MAplot",
        "MAplot,CuffData-method"
      ]
    },
    {
      "page": "PINK1",
      "title": "PINK1",
      "topics": [
        "PINK1"
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    },
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