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  "Package": "RFLOMICS",
  "Title": "Interactive web application for Omics-data analysis",
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  "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",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:47 UTC",
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  "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]",
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  "_created": "2026-11-01T14:18:15.000Z",
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        "key": "RFLOMICS::generic:runTransformData",
        "hash": "e1eb351c86f24a19"
      },
      {
        "key": "RFLOMICS::generic:setElementToMetadata",
        "hash": "7aa86f3082be8604"
      },
      {
        "key": "RFLOMICS::generic:setMOFA",
        "hash": "063059c03b13d203"
      },
      {
        "key": "RFLOMICS::generic:setMixOmics",
        "hash": "c4726e170fca28dc"
      },
      {
        "key": "RFLOMICS::generic:setModelFormula",
        "hash": "1934307773445374"
      },
      {
        "key": "RFLOMICS::generic:setSelectedContrasts",
        "hash": "1f2778021fc40ce8"
      },
      {
        "key": "RFLOMICS::generic:setValidContrasts",
        "hash": "a5933fc04c82c7b5"
      },
      {
        "key": "RFLOMICS::generic:subRflomicsMAE",
        "hash": "6ea4094d668533cf"
      },
      {
        "key": "RFLOMICS::generic:sumMixOmics",
        "hash": "d6ea60b80eb1f290"
      },
      {
        "key": "RFLOMICS::generic:sumORA",
        "hash": "168fb576e67dec36"
      }
    ],
    "imports": [
      {
        "key": "MultiAssayExperiment::MultiAssayExperiment",
        "hash": "9784902179b4174c"
      },
      {
        "key": "S4Vectors::Annotated",
        "hash": "9b5b8ee6ad9969f8"
      },
      {
        "key": "S4Vectors::RectangularData",
        "hash": "d414a10823a4aada"
      },
      {
        "key": "S4Vectors::Vector",
        "hash": "09cab0bd77ae353b"
      },
      {
        "key": "S4Vectors::vector_OR_Vector",
        "hash": "f3fc18c9f8ff2633"
      },
      {
        "key": "SummarizedExperiment::SummarizedExperiment",
        "hash": "d53ca73257d1e8cf"
      }
    ]
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/RFLOMICS.html"
  ],
  "_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",
        "getTransSettings",
        "getTransSettings,RflomicsMAE-method",
        "getTransSettings,RflomicsSE-method",
        "isProcessedData",
        "isProcessedData,RflomicsMAE-method",
        "isProcessedData,RflomicsSE-method",
        "plotDataDistribution",
        "plotDataDistribution,RflomicsMAE-method",
        "plotDataDistribution,RflomicsSE-method",
        "plotExpDesignCompleteness",
        "plotExpDesignCompleteness,RflomicsMAE-method",
        "plotExpDesignCompleteness,RflomicsSE-method",
        "plotLibrarySize",
        "plotLibrarySize,RflomicsMAE-method",
        "plotLibrarySize,RflomicsSE-method",
        "plotMissingValues",
        "plotMissingValues,RflomicsMAE-method",
        "plotMissingValues,RflomicsSE-method",
        "plotOmicsPCA",
        "plotOmicsPCA,RflomicsMAE-method",
        "plotOmicsPCA,RflomicsSE-method",
        "runDataProcessing",
        "runDataProcessing,RflomicsMAE-method",
        "runDataProcessing,RflomicsSE-method",
        "runFeatureFiltering",
        "runFeatureFiltering,RflomicsMAE-method",
        "runFeatureFiltering,RflomicsSE-method",
        "runMVImputation",
        "runMVImputation,RflomicsMAE-method",
        "runMVImputation,RflomicsSE-method",
        "runNormalization",
        "runNormalization,RflomicsMAE-method",
        "runNormalization,RflomicsSE-method",
        "runOmicsPCA",
        "runOmicsPCA,RflomicsMAE-method",
        "runOmicsPCA,RflomicsSE-method",
        "runSampleFiltering",
        "runSampleFiltering,RflomicsMAE-method",
        "runSampleFiltering,RflomicsSE-method",
        "runTransformData",
        "runTransformData,RflomicsMAE-method",
        "runTransformData,RflomicsSE-method"
      ]
    },
    {
      "page": "runDiffAnalysis",
      "title": "Run Differential Expression Analysis and process results",
      "topics": [
        "filterDiffAnalysis",
        "filterDiffAnalysis,RflomicsMAE-method",
        "filterDiffAnalysis,RflomicsSE-method",
        "getDEList",
        "getDEList,RflomicsMAE-method",
        "getDEList,RflomicsSE-method",
        "getDEMatrix",
        "getDEMatrix,RflomicsMAE-method",
        "getDEMatrix,RflomicsSE-method",
        "getDiffAnalysesSummary",
        "getDiffAnalysesSummary,RflomicsMAE-method",
        "getDiffSettings",
        "getDiffSettings,RflomicsMAE-method",
        "getDiffSettings,RflomicsSE-method",
        "getDiffStat",
        "getDiffStat,RflomicsMAE-method",
        "getDiffStat,RflomicsSE-method",
        "getValidContrasts",
        "getValidContrasts,RflomicsMAE-method",
        "getValidContrasts,RflomicsSE-method",
        "plotBoxplotDE",
        "plotBoxplotDE,RflomicsMAE-method",
        "plotBoxplotDE,RflomicsSE-method",
        "plotDiffAnalysis",
        "plotDiffAnalysis,RflomicsMAE-method",
        "plotDiffAnalysis,RflomicsSE-method",
        "plotHeatmapDesign",
        "plotHeatmapDesign,RflomicsMAE-method",
        "plotHeatmapDesign,RflomicsSE-method",
        "runDiffAnalysis",
        "runDiffAnalysis,RflomicsMAE-method",
        "runDiffAnalysis,RflomicsSE-method",
        "setValidContrasts",
        "setValidContrasts,RflomicsMAE-method",
        "setValidContrasts,RflomicsSE-method"
      ]
    },
    {
      "page": "runOmicsIntegration",
      "title": "runOmicsIntegration",
      "topics": [
        "getMixOmics",
        "getMixOmics,RflomicsMAE-method",
        "getMixOmicsSettings",
        "getMixOmicsSettings,RflomicsMAE-method",
        "getMOFA",
        "getMOFA,RflomicsMAE-method",
        "getMOFASettings",
        "getMOFASettings,RflomicsMAE-method",
        "runOmicsIntegration",
        "runOmicsIntegration,RflomicsMAE-method",
        "setMixOmics",
        "setMixOmics,RflomicsMAE-method",
        "setMOFA",
        "setMOFA,RflomicsMAE-method",
        "sumMixOmics",
        "sumMixOmics,RflomicsMAE-method"
      ]
    },
    {
      "page": "runRFLOMICS",
      "title": "Run RFLOMICS interface",
      "topics": [
        "runRFLOMICS"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/RFLOMICS/raw/HEAD/README.md",
  "_rundeps": [
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    "aisdk",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "backports",
    "base64enc",
    "basilisk",
    "bayesm",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "biocmake",
    "BiocParallel",
    "Biostrings",
    "bit",
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    "blob",
    "boot",
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    "bslib",
    "cachem",
    "callr",
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    "corrplot",
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    "digest",
    "dir.expiry",
    "doBy",
    "doParallel",
    "DOSE",
    "dplyr",
    "dqrng",
    "DT",
    "e1071",
    "edgeR",
    "ellipse",
    "emmeans",
    "enrichit",
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    "evaluate",
    "FactoMineR",
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    "filelock",
    "flashClust",
    "FNN",
    "fontawesome",
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    "fontLiberation",
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    "GlobalOptions",
    "glue",
    "GO.db",
    "GOSemSim",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "h5mread",
    "HDF5Array",
    "here",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "HTSCluster",
    "HTSFilter",
    "httpuv",
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    "igraph",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
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    "later",
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    "lifecycle",
    "limma",
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    "magrittr",
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    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "minqa",
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    "modelr",
    "MOFA2",
    "multcompView",
    "MultiAssayExperiment",
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    "org.At.tair.db",
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    "pkgconfig",
    "plotly",
    "plotrix",
    "plyr",
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    "polyclip",
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    "promises",
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    "rhdf5filters",
    "Rhdf5lib",
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    "robustbase",
    "rprojroot",
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    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "scatterplot3d",
    "Seqinfo",
    "shape",
    "shiny",
    "shinyBS",
    "shinydashboard",
    "shinyWidgets",
    "showtext",
    "showtextdb",
    "sitmo",
    "sna",
    "snow",
    "sourcetools",
    "SparseArray",
    "SparseM",
    "statmod",
    "statnet.common",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "sysfonts",
    "systemfonts",
    "tensorA",
    "tibble",
    "tidydr",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timeDate",
    "tinytex",
    "treeio",
    "tweenr",
    "tzdb",
    "UpSetR",
    "urca",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "vroom",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "RFLOMICS.Rmd",
      "filename": "RFLOMICS.html",
      "title": "RFLOMICS",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install and run RFLOMICS",
        "Guided tour of the interface",
        "Load Data",
        "Dataset example description",
        "Load Experimental Design",
        "Load Omics data",
        "Set the statistical framework",
        "Single omics data analysis",
        "Data processing and quality check",
        "Completeness check",
        "Transcriptomics data",
        "Differential expression analysis",
        "Coexpression analysis",
        "Annotation and Enrichment analysis using clusterProfiler",
        "Dataset analysis summary",
        "Integration",
        "MOFA",
        "MixOmics",
        "Exploring results from RFLOMICS",
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