{
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  "Package": "biosigner",
  "Type": "Package",
  "Title": "Signature discovery from omics data",
  "Version": "1.41.0",
  "Date": "2025-07-02",
  "Authors@R": "c(person(\"Philippe\", \"Rinaudo\", email = \"phd.rinaudo@gmail.com\", role = c(\"aut\")),\nperson(\"Etienne A.\", \"Thevenot\", email = \"etienne.thevenot@cea.fr\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-1019-4577\")))",
  "Maintainer": "Etienne A. Thevenot <etienne.thevenot@cea.fr>",
  "biocViews": "Classification, FeatureExtraction, Transcriptomics,\nProteomics, Metabolomics, Lipidomics, MassSpectrometry",
  "Description": "Feature selection is critical in omics data analysis to\nextract restricted and meaningful molecular signatures from\ncomplex and high-dimension data, and to build robust\nclassifiers. This package implements a new method to assess the\nrelevance of the variables for the prediction performances of\nthe classifier. The approach can be run in parallel with the\nPLS-DA, Random Forest, and SVM binary classifiers. The\nsignatures and the corresponding 'restricted' models are\nreturned, enabling future predictions on new datasets. A Galaxy\nimplementation of the package is available within the\nWorkflow4metabolomics.org online infrastructure for\ncomputational metabolomics.",
  "VignetteBuilder": "knitr",
  "License": "CeCILL",
  "Encoding": "UTF-8",
  "LazyLoad": "yes",
  "URL": "http://dx.doi.org/10.3389/fmolb.2016.00026",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:41:55 UTC",
    "User": "root"
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:51 UTC",
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  "Author": "Philippe Rinaudo [aut],\nEtienne A. Thevenot [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-1019-4577>)",
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  "_cranurl": false,
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    "getBiosign",
    "getEset",
    "getMset",
    "getSignatureLs",
    "plot",
    "predict",
    "show"
  ],
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      "tojson": true
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    {
      "page": "biosigner-package",
      "title": "Molecular signature discovery from omics data",
      "topics": [
        "biosigner-package",
        "biosigner"
      ]
    },
    {
      "page": "biosign",
      "title": "Builds the molecular signature.",
      "topics": [
        "biosign",
        "biosign,data.frame-method",
        "biosign,ExpressionSet-method",
        "biosign,matrix-method",
        "biosign,MultiAssayExperiment-method",
        "biosign,MultiDataSet-method",
        "biosign,MultiDataSet_method",
        "biosign,SummarizedExperiment-method"
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    },
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      "page": "biosign-class",
      "title": "Class \"biosign\"",
      "topics": [
        "biosign-class"
      ]
    },
    {
      "page": "biosignMultiDataSet-class",
      "title": "Class \"biosignMultiDataSet\"",
      "topics": [
        "biosignMultiDataSet-class"
      ]
    },
    {
      "page": "diaplasma",
      "title": "Analysis of plasma from diabetic patients by LC-HRMS",
      "topics": [
        "diaplasma"
      ]
    },
    {
      "page": "getAccuracyMN",
      "title": "Accuracies of the full model and the models restricted to the signatures",
      "topics": [
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        "getAccuracyMN,biosign-method"
      ]
    },
    {
      "page": "getBiosign",
      "title": "Getting the biosigner signature from the SummarizedExperiment object",
      "topics": [
        "getBiosign",
        "getBiosign,MultiAssayExperiment-method",
        "getBiosign,SummarizedExperiment-method"
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      "title": "getEset method",
      "topics": [
        "biosign-method",
        "getEset",
        "getEset,",
        "getEset,biosign-method"
      ]
    },
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      "topics": [
        "biosignMultiDataSet-method",
        "getMset",
        "getMset,",
        "getMset,biosignMultiDataSet-method"
      ]
    },
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      "title": "Signatures selected by the models",
      "topics": [
        "getSignatureLs",
        "getSignatureLs,biosign-method"
      ]
    },
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      "page": "plot",
      "title": "Plot method for 'biosign' signature objects",
      "topics": [
        "plot,biosign,ANY-method",
        "plot,biosign-method",
        "plot,biosignMultiDataSet,ANY-method",
        "plot,biosignMultiDataSet-method",
        "plot.biosign",
        "plot.biosignMultiDataSet"
      ]
    },
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      "title": "Predict method for 'biosign' signature objects",
      "topics": [
        "predict,biosign-method",
        "predict.biosign"
      ]
    },
    {
      "page": "show",
      "title": "Show method for 'biosign' signature objects",
      "topics": [
        "show,biosign-method",
        "show.biosign"
      ]
    },
    {
      "page": "SpikePos",
      "title": "Spike-in metabolomics data for apple extracts (from the BioMark package)",
      "topics": [
        "SpikePos"
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      "title": "biosigner: A new method for signature discovery from omics data",
      "author": "Philippe Rinaudo and Etienne Thevenot",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "The biosigner package",
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        "Molecular signatures",
        "Predictions",
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        "ExpressionSet format",
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        "MultiDataSet objects",
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        "Physiological variations of the human urine metabolome (metabolomics)",
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        "Bone marrow from acute leukemia patients (transcriptomics)",
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      "created": "2016-09-18 13:05:05",
      "modified": "2025-06-23 20:37:20",
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