{
  "_id": "6a1af2b81d7bb097a09f7d17",
  "Package": "RFLOMICS",
  "Title": "Interactive web application for Omics-data analysis",
  "Version": "1.5.0",
  "Authors@R": "c(\nperson(given = \"Nadia\", family = \"Bessoltane\",\nemail = \"nadia.bessoltane@inrae.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID=\"0000-0001-6931-2529\")),\nperson(given = \"Delphine\", family = \"Charif\",\nemail = \"delphine.charif@inrae.fr\", role = c(\"aut\"),\ncomment = c(ORCID=\"0000-0002-1949-5969\")),\nperson(given = \"Audrey\", family = \"Hulot\",\nemail = \"audrey.hulot@inrae.fr\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9647-6470\")),\nperson(given = \"Christine\", family = \"Paysant-Leroux\",\nemail = \"christine.paysant-le-roux@inrae.fr\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2046-6492\")),\nperson(given = \"Gwendal\", family = \"Cueff\",\nemail = \"gwendal.cueff@inrae.fr\", role = c(\"aut\"))\n)",
  "Description": "R-package with shiny interface, provides a framework for\nthe analysis of transcriptomics, proteomics and/or metabolomics\ndata. The interface offers a guided experience for the user,\nfrom the definition of the experimental design to the\nintegration of several omics table together. A report can be\ngenerated with all settings and analysis results.",
  "URL": "https://github.com/RFLOMICS/RFLOMICS",
  "BugReports": "https://github.com/RFLOMICS/RFLOMICS/issues",
  "biocViews": "ShinyApps, DifferentialExpression, Metabolomics, Proteomics,\nTranscriptomics",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "SystemRequirements": "Python (>=3), numpy, pandas, h5py, scipy, argparse,\nsklearn, mofapy2 (>=0.7.1)",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev libglu1-mesa-dev make texlive\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libgl1-mesa-dev\nlibssl-dev perl python3 zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:47 UTC",
  "RemoteUrl": "https://github.com/bioc/RFLOMICS",
  "RemoteRef": "HEAD",
  "RemoteSha": "f2a9e772561d6b28fd97fe0bbe506d2dd970dd7b",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:43:25 UTC",
    "User": "root"
  },
  "Author": "Nadia Bessoltane [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6931-2529>),\nDelphine Charif [aut] (ORCID: <https://orcid.org/0000-0002-1949-5969>),\nAudrey Hulot [aut] (ORCID: <https://orcid.org/0000-0002-9647-6470>),\nChristine Paysant-Leroux [aut] (ORCID:\n<https://orcid.org/0000-0003-2046-6492>),\nGwendal Cueff [aut]",
  "Maintainer": "Nadia Bessoltane <nadia.bessoltane@inrae.fr>",
  "MD5sum": "700879bd5ac0caa4daa4a4ddae203508",
  "_user": "bioc",
  "_type": "src",
  "_file": "RFLOMICS_1.5.0.tar.gz",
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  "_filesize": 5115300,
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  "_created": "2026-05-30T09:43:25.000Z",
  "_published": "2026-05-30T14:22:48.855Z",
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  "_topics": [
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    "differentialexpression",
    "metabolomics",
    "proteomics",
    "transcriptomics"
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    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/RFLOMICS"
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  "_devurl": "https://github.com/rflomics/rflomics",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
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    "extra/contents.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
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    "manual.pdf"
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  "_homeurl": "https://github.com/rflomics/rflomics",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkExpDesignCompleteness",
    "createRflomicsMAE",
    "filterDiffAnalysis",
    "generateExpressionContrast",
    "generateModelFormulae",
    "generateReport",
    "getAnalysis",
    "getAnalyzedDatasetNames",
    "getAnnotAnalysesSummary",
    "getBatchFactors",
    "getBioFactors",
    "getCoeffNorm",
    "getCoExpAnalysesSummary",
    "getCoexpClusters",
    "getCoexpSettings",
    "getDatasetNames",
    "getDEList",
    "getDEMatrix",
    "getDesignMat",
    "getDiffAnalysesSummary",
    "getDiffSettings",
    "getDiffStat",
    "getEnrichRes",
    "getEnrichSettings",
    "getFactorModalities",
    "getFactorNames",
    "getFactorTypes",
    "getFilteredFeatures",
    "getFilterSettings",
    "getImputSettings",
    "getMetaFactors",
    "getMixOmics",
    "getMixOmicsSettings",
    "getModelFormula",
    "getMOFA",
    "getMOFASettings",
    "getNormSettings",
    "getOmicsTypes",
    "getProcessedData",
    "getProjectName",
    "getRflomicsSE",
    "getSelectedContrasts",
    "getSelectedSamples",
    "getTransSettings",
    "getValidContrasts",
    "isProcessedData",
    "plotBoxplotDE",
    "plotClusterProfiler",
    "plotCoExpression",
    "plotCoExpressionProfile",
    "plotConditionsOverview",
    "plotCoseqContrasts",
    "plotDataDistribution",
    "plotDataOverview",
    "plotDiffAnalysis",
    "plotEnrichComp",
    "plotExpDesignCompleteness",
    "plotHeatmapDesign",
    "plotLibrarySize",
    "plotMissingValues",
    "plotOmicsPCA",
    "prepareForIntegration",
    "rflomicsMAE2MAE",
    "runAnnotationEnrichment",
    "runCoExpression",
    "runDataProcessing",
    "runDiffAnalysis",
    "runFeatureFiltering",
    "runMVImputation",
    "runNormalization",
    "runOmicsIntegration",
    "runOmicsPCA",
    "runRFLOMICS",
    "runSampleFiltering",
    "runTransformData",
    "setMixOmics",
    "setModelFormula",
    "setMOFA",
    "setSelectedContrasts",
    "setValidContrasts",
    "subRflomicsMAE",
    "sumMixOmics",
    "sumORA"
  ],
  "_datasets": [
    {
      "name": "ecoseed.df",
      "title": "Ecoseed project data",
      "object": "ecoseed.df",
      "file": "ecoseed.df.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ecoseed.mae",
      "title": "Ecoseed project data",
      "object": "ecoseed.mae",
      "file": "ecoseed.mae.rda",
      "class": [
        "MultiAssayExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "createRflomicsMAE",
      "title": "RflomicsMAE class constructor",
      "topics": [
        "createRflomicsMAE"
      ]
    },
    {
      "page": "ecoseed.df",
      "title": "Ecoseed project data",
      "topics": [
        "ecoseed.df"
      ]
    },
    {
      "page": "ecoseed.mae",
      "title": "Ecoseed project data",
      "topics": [
        "ecoseed.mae"
      ]
    },
    {
      "page": "generateExpressionContrast",
      "title": "Contrast expressions",
      "topics": [
        "generateExpressionContrast",
        "generateExpressionContrast,RflomicsMAE-method",
        "generateExpressionContrast,RflomicsSE-method",
        "getSelectedContrasts",
        "getSelectedContrasts,RflomicsMAE-method",
        "getSelectedContrasts,RflomicsSE-method",
        "setSelectedContrasts",
        "setSelectedContrasts,RflomicsMAE-method",
        "setSelectedContrasts,RflomicsSE-method"
      ]
    },
    {
      "page": "generateModelFormulae",
      "title": "Statistical model formulae",
      "topics": [
        "generateModelFormulae",
        "generateModelFormulae,RflomicsMAE-method",
        "getModelFormula",
        "getModelFormula,RflomicsMAE-method",
        "getModelFormula,RflomicsSE-method",
        "setModelFormula",
        "setModelFormula,RflomicsMAE-method",
        "setModelFormula,RflomicsSE-method"
      ]
    },
    {
      "page": "generateReport",
      "title": "Generate RFLOMICS html report or archive",
      "topics": [
        "generateReport",
        "generateReport,RflomicsMAE-method"
      ]
    },
    {
      "page": "getAnalysis",
      "title": "Get results from RFLOMICS object",
      "topics": [
        "getAnalysis",
        "getAnalysis,RflomicsMAE-method",
        "getAnalysis,RflomicsSE-method",
        "getAnalyzedDatasetNames",
        "getAnalyzedDatasetNames,RflomicsMAE-method"
      ]
    },
    {
      "page": "prepareForIntegration",
      "title": "Preparation step for integration",
      "topics": [
        "prepareForIntegration",
        "prepareForIntegration,RflomicsMAE-method"
      ]
    },
    {
      "page": "RflomicsMAE-class",
      "title": "RflomicsMAE Class",
      "topics": [
        "getBatchFactors",
        "getBatchFactors,RflomicsMAE-method",
        "getBioFactors",
        "getBioFactors,RflomicsMAE-method",
        "getDatasetNames",
        "getDatasetNames,RflomicsMAE-method",
        "getDesignMat",
        "getDesignMat,RflomicsMAE-method",
        "getFactorModalities",
        "getFactorModalities,RflomicsMAE-method",
        "getFactorNames",
        "getFactorNames,RflomicsMAE-method",
        "getFactorTypes",
        "getFactorTypes,RflomicsMAE-method",
        "getMetaFactors",
        "getMetaFactors,RflomicsMAE-method",
        "getOmicsTypes",
        "getOmicsTypes,RflomicsMAE-method",
        "getProjectName",
        "getProjectName,RflomicsMAE-method",
        "getRflomicsSE",
        "getRflomicsSE,RflomicsMAE-method",
        "plotConditionsOverview",
        "plotConditionsOverview,RflomicsMAE-method",
        "plotDataOverview",
        "plotDataOverview,RflomicsMAE-method",
        "RflomicsMAE-class",
        "subRflomicsMAE",
        "subRflomicsMAE,RflomicsMAE-method"
      ]
    },
    {
      "page": "rflomicsMAE2MAE",
      "title": "convert a RflomicsMAE to a MultiAssayExperiment",
      "topics": [
        "rflomicsMAE2MAE",
        "rflomicsMAE2MAE,RflomicsMAE-method"
      ]
    },
    {
      "page": "RflomicsSE-class",
      "title": "RflomicsSE Class",
      "topics": [
        "getBatchFactors,RflomicsSE-method",
        "getBioFactors,RflomicsSE-method",
        "getDatasetNames,RflomicsSE-method",
        "getDesignMat,RflomicsSE-method",
        "getFactorModalities,RflomicsSE-method",
        "getFactorNames,RflomicsSE-method",
        "getFactorTypes,RflomicsSE-method",
        "getMetaFactors,RflomicsSE-method",
        "getOmicsTypes,RflomicsSE-method",
        "RflomicsSE",
        "RflomicsSE-class"
      ]
    },
    {
      "page": "runAnnotationEnrichment",
      "title": "Run Gene Enrichment Analysis and process results",
      "topics": [
        "getAnnotAnalysesSummary",
        "getAnnotAnalysesSummary,RflomicsMAE-method",
        "getEnrichRes",
        "getEnrichRes,RflomicsMAE-method",
        "getEnrichRes,RflomicsSE-method",
        "getEnrichSettings",
        "getEnrichSettings,RflomicsSE-method",
        "plotClusterProfiler",
        "plotClusterProfiler,RflomicsSE-method",
        "plotEnrichComp",
        "plotEnrichComp,RflomicsSE-method",
        "runAnnotationEnrichment",
        "runAnnotationEnrichment,RflomicsMAE-method",
        "runAnnotationEnrichment,RflomicsSE-method",
        "sumORA",
        "sumORA,RflomicsSE-method"
      ]
    },
    {
      "page": "runCoExpression",
      "title": "Run CoExpression Analysis and process results",
      "topics": [
        "getCoExpAnalysesSummary",
        "getCoExpAnalysesSummary,RflomicsMAE-method",
        "getCoexpClusters",
        "getCoexpClusters,RflomicsMAE-method",
        "getCoexpClusters,RflomicsSE-method",
        "getCoexpSettings",
        "getCoexpSettings,RflomicsMAE-method",
        "getCoexpSettings,RflomicsSE-method",
        "plotCoExpression",
        "plotCoExpression,RflomicsMAE-method",
        "plotCoExpression,RflomicsSE-method",
        "plotCoExpressionProfile",
        "plotCoExpressionProfile,RflomicsMAE-method",
        "plotCoExpressionProfile,RflomicsSE-method",
        "plotCoseqContrasts",
        "plotCoseqContrasts,RflomicsMAE-method",
        "plotCoseqContrasts,RflomicsSE-method",
        "runCoExpression",
        "runCoExpression,RflomicsMAE-method",
        "runCoExpression,RflomicsSE-method"
      ]
    },
    {
      "page": "runDataProcessing",
      "title": "Omic Data Exploratory and Preprocessing",
      "topics": [
        "checkExpDesignCompleteness",
        "checkExpDesignCompleteness,RflomicsMAE-method",
        "checkExpDesignCompleteness,RflomicsSE-method",
        "getCoeffNorm",
        "getCoeffNorm,RflomicsMAE-method",
        "getCoeffNorm,RflomicsSE-method",
        "getFilteredFeatures",
        "getFilteredFeatures,RflomicsMAE-method",
        "getFilteredFeatures,RflomicsSE-method",
        "getFilterSettings",
        "getFilterSettings,RflomicsMAE-method",
        "getFilterSettings,RflomicsSE-method",
        "getImputSettings",
        "getImputSettings,RflomicsMAE-method",
        "getImputSettings,RflomicsSE-method",
        "getNormSettings",
        "getNormSettings,RflomicsMAE-method",
        "getNormSettings,RflomicsSE-method",
        "getProcessedData",
        "getProcessedData,RflomicsMAE-method",
        "getProcessedData,RflomicsSE-method",
        "getSelectedSamples",
        "getSelectedSamples,RflomicsMAE-method",
        "getSelectedSamples,RflomicsSE-method",
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