{
  "_id": "6a1ab0511d7bb097a09d5759",
  "Package": "ReducedExperiment",
  "Type": "Package",
  "Title": "Containers and tools for dimensionally-reduced -omics\nrepresentations",
  "Version": "1.5.0",
  "Authors@R": "c(\nperson(\"Jack\", \"Gisby\", , \"jackgisby@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-0511-8123\")),\nperson(\"Michael\", \"Barnes\", , \"m.r.barnes@qmul.ac.uk\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-9097-7381\"))\n)",
  "Date": "2024-07-30",
  "Description": "Provides SummarizedExperiment-like containers for storing\nand manipulating dimensionally-reduced assay data. The\nReducedExperiment classes allow users to simultaneously\nmanipulate their original dataset and their decomposed data, in\naddition to other method-specific outputs like feature\nloadings. Implements utilities and specialised classes for the\napplication of stabilised independent component analysis (sICA)\nand weighted gene correlation network analysis (WGCNA).",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/jackgisby/ReducedExperiment",
  "BugReports": "https://github.com/jackgisby/ReducedExperiment/issues",
  "biocViews": "GeneExpression, Infrastructure, DataRepresentation,\nSoftware, DimensionReduction, Network",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:04:10 UTC",
  "RemoteUrl": "https://github.com/bioc/ReducedExperiment",
  "RemoteRef": "HEAD",
  "RemoteSha": "a184d2159b5f96da0bd5c540a1250bb4e0f801a9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:03:30 UTC",
    "User": "root"
  },
  "Author": "Jack Gisby [aut, cre] (ORCID: <https://orcid.org/0000-0003-0511-8123>),\nMichael Barnes [aut] (ORCID: <https://orcid.org/0000-0001-9097-7381>)",
  "Maintainer": "Jack Gisby <jackgisby@gmail.com>",
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  "_created": "2026-05-30T07:03:30.000Z",
  "_published": "2026-05-30T09:39:29.503Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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      "n": 2
    },
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
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      "bioc": "3.24"
    },
    {
      "branch": "release",
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      "bioc": "3.23"
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  ],
  "_topics": [
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    "infrastructure",
    "datarepresentation",
    "software",
    "dimensionreduction",
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    "bioconductor-package",
    "bioinformatics",
    "dimensionality-reduction"
  ],
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      "count": 259,
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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/ReducedExperiment"
  },
  "_devurl": "https://github.com/jackgisby/reducedexperiment",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/ReducedExperiment.html",
    "manual.pdf"
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  "_homeurl": "https://github.com/jackgisby/reducedexperiment",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assessSoftThreshold",
    "assignments",
    "assignments<-",
    "associateComponents",
    "calcEigengenes",
    "cbind",
    "colnames<-",
    "componentNames",
    "componentNames<-",
    "dendrogram",
    "dendrogram<-",
    "estimateFactors",
    "estimateStability",
    "FactorisedExperiment",
    "featureNames",
    "featureNames<-",
    "getAlignedFeatures",
    "getCentrality",
    "getCommonFeatures",
    "getGeneIDs",
    "getMsigdbT2G",
    "identifyModules",
    "loadings",
    "loadings<-",
    "ModularExperiment",
    "moduleNames",
    "moduleNames<-",
    "modulePreservation",
    "nComponents",
    "nFeatures",
    "nModules",
    "nSamples",
    "plotCommonFeatures",
    "plotDendro",
    "plotModulePreservation",
    "plotStability",
    "predict",
    "projectData",
    "rbind",
    "reduced",
    "reduced<-",
    "ReducedExperiment",
    "rownames<-",
    "ROWNAMES<-",
    "runEnrich",
    "runICA",
    "runWGCNA",
    "sampleNames",
    "sampleNames<-",
    "show",
    "stability",
    "stability<-"
  ],
  "_help": [
    {
      "page": "dollar_names",
      "title": "Command line completion for '$'",
      "topics": [
        ".DollarNames.FactorisedExperiment",
        ".DollarNames.ModularExperiment",
        ".DollarNames.ReducedExperiment",
        "dollar_names"
      ]
    },
    {
      "page": "slice",
      "title": "Extract and replace parts of ReducedExperiment objects",
      "topics": [
        "slice",
        "[,FactorisedExperiment,ANY,ANY,ANY-method",
        "[,ModularExperiment,ANY,ANY,ANY-method",
        "[,ReducedExperiment,ANY,ANY,ANY-method",
        "[<-,FactorisedExperiment,ANY,ANY,FactorisedExperiment-method",
        "[<-,ModularExperiment,ANY,ANY,ModularExperiment-method",
        "[<-,ReducedExperiment,ANY,ANY,ReducedExperiment-method"
      ]
    },
    {
      "page": "assessSoftThreshold",
      "title": "Assess soft thresholding power for WGCNA",
      "topics": [
        "assessSoftThreshold"
      ]
    },
    {
      "page": "module_assignments",
      "title": "Get and set module feature assignments",
      "topics": [
        "assignments",
        "assignments,ModularExperiment-method",
        "assignments<-",
        "assignments<-,ModularExperiment-method"
      ]
    },
    {
      "page": "associateComponents",
      "title": "Runs linear models for components and sample-level data",
      "topics": [
        "associateComponents"
      ]
    },
    {
      "page": "calcEigengenes",
      "title": "Calculate eigengenes for new data",
      "topics": [
        "calcEigengenes",
        "calcEigengenes,ModularExperiment,data.frame-method",
        "calcEigengenes,ModularExperiment,matrix-method",
        "calcEigengenes,ModularExperiment,SummarizedExperiment-method",
        "predict,ModularExperiment-method"
      ]
    },
    {
      "page": "cbind_rbind",
      "title": "Combine ReducedExperiment objects by columns or rows",
      "topics": [
        "cbind,FactorisedExperiment-method",
        "cbind,ModularExperiment-method",
        "cbind,ReducedExperiment-method",
        "cbind_rbind",
        "rbind,FactorisedExperiment-method",
        "rbind,ModularExperiment-method",
        "rbind,ReducedExperiment-method"
      ]
    },
    {
      "page": "component_names",
      "title": "Get names of dimensionally-reduced components",
      "topics": [
        "componentNames",
        "componentNames,ReducedExperiment-method",
        "componentNames<-",
        "componentNames<-,FactorisedExperiment-method",
        "componentNames<-,ModularExperiment-method",
        "componentNames<-,ReducedExperiment-method",
        "moduleNames",
        "moduleNames,ModularExperiment-method",
        "moduleNames<-",
        "moduleNames<-,ModularExperiment-method"
      ]
    },
    {
      "page": "module_dendrogram",
      "title": "Get the dendrogram stored in a ModularExperiment",
      "topics": [
        "dendrogram",
        "dendrogram,ModularExperiment-method",
        "dendrogram<-",
        "dendrogram<-,ModularExperiment-method"
      ]
    },
    {
      "page": "dim-ReducedExperiment-method",
      "title": "Get the dimensions of a Reducedexperiment object",
      "topics": [
        "dim,ReducedExperiment-method"
      ]
    },
    {
      "page": "estimateFactors",
      "title": "Perform dimensionality reduction using Independent Component Analysis",
      "topics": [
        "estimateFactors"
      ]
    },
    {
      "page": "estimateStability",
      "title": "Estimate stability of factors as a function of the number of components",
      "topics": [
        "estimateStability"
      ]
    },
    {
      "page": "factorised_experiment",
      "title": "FactorisedExperiment: A container for the results of factor analysis",
      "topics": [
        ".FactorisedExperiment",
        "FactorisedExperiment",
        "FactorisedExperiment-class"
      ]
    },
    {
      "page": "getAlignedFeatures",
      "title": "Get feature alignments with factors",
      "topics": [
        "getAlignedFeatures",
        "getAlignedFeatures,FactorisedExperiment-method"
      ]
    },
    {
      "page": "getCentrality",
      "title": "Get correlation of features with module eigengenes",
      "topics": [
        "getCentrality",
        "getCentrality,ModularExperiment-method"
      ]
    },
    {
      "page": "getCommonFeatures",
      "title": "Get common factor features",
      "topics": [
        "getCommonFeatures"
      ]
    },
    {
      "page": "get_gene_ids",
      "title": "Gets alternative gene annotations from biomaRt",
      "topics": [
        "getGeneIDs",
        "getGeneIDs,ReducedExperiment-method"
      ]
    },
    {
      "page": "getMsigdbT2G",
      "title": "Get TERM2GENE dataframe from MSigDB",
      "topics": [
        "getMsigdbT2G"
      ]
    },
    {
      "page": "identifyModules",
      "title": "Apply dimensionality reduction using Weighted Gene Correlation Network Analysis",
      "topics": [
        "identifyModules"
      ]
    },
    {
      "page": "loadings",
      "title": "Get and set loadings",
      "topics": [
        "loadings",
        "loadings,FactorisedExperiment-method",
        "loadings,ModularExperiment-method",
        "loadings<-",
        "loadings<-,FactorisedExperiment-method",
        "loadings<-,ModularExperiment-method"
      ]
    },
    {
      "page": "modular_experiment",
      "title": "ModularExperiment: A container for the results of module analysis",
      "topics": [
        ".ModularExperiment",
        "ModularExperiment",
        "ModularExperiment-class"
      ]
    },
    {
      "page": "modulePreservation",
      "title": "Get module preservation statistics",
      "topics": [
        "modulePreservation"
      ]
    },
    {
      "page": "feature_names",
      "title": "Get feature names",
      "topics": [
        "featureNames",
        "featureNames,ReducedExperiment-method",
        "featureNames<-",
        "featureNames<-,FactorisedExperiment-method",
        "featureNames<-,ModularExperiment-method",
        "featureNames<-,ReducedExperiment-method",
        "names<-,FactorisedExperiment-method",
        "names<-,ModularExperiment-method",
        "names<-,ReducedExperiment-method",
        "rownames<-,FactorisedExperiment-method",
        "rownames<-,ModularExperiment-method",
        "ROWNAMES<-,ReducedExperiment-method",
        "rownames<-,ReducedExperiment-method"
      ]
    },
    {
      "page": "individual_dims",
      "title": "Prints individual lengths of samples, components and features",
      "topics": [
        "individual_dim",
        "nComponents",
        "nComponents,ReducedExperiment-method",
        "nFeatures",
        "nFeatures,ReducedExperiment-method",
        "nModules",
        "nModules,ModularExperiment-method",
        "nSamples",
        "nSamples,ReducedExperiment-method"
      ]
    },
    {
      "page": "plotCommonFeatures",
      "title": "Heatmap comparing commonality across factors",
      "topics": [
        "plotCommonFeatures"
      ]
    },
    {
      "page": "plotDendro",
      "title": "Plot a dendrogram stored in a ModularExperiment",
      "topics": [
        "plotDendro",
        "plotDendro,ModularExperiment-method"
      ]
    },
    {
      "page": "plotModulePreservation",
      "title": "Plot module preservation statistics",
      "topics": [
        "plotModulePreservation"
      ]
    },
    {
      "page": "plotStability",
      "title": "Plot component stability as a function of the number of components",
      "topics": [
        "plotStability"
      ]
    },
    {
      "page": "projectData",
      "title": "Project new data using pre-defined factors",
      "topics": [
        "predict,FactorisedExperiment-method",
        "projectData",
        "projectData,FactorisedExperiment,data.frame-method",
        "projectData,FactorisedExperiment,matrix-method",
        "projectData,FactorisedExperiment,SummarizedExperiment-method"
      ]
    },
    {
      "page": "reduced",
      "title": "Get and set reduced data",
      "topics": [
        "reduced",
        "reduced,ReducedExperiment-method",
        "reduced<-",
        "reduced<-,ReducedExperiment-method"
      ]
    },
    {
      "page": "reduced_experiment",
      "title": "ReducedExperiment: A container for dimensionally-reduced representations",
      "topics": [
        ".ReducedExperiment",
        "ReducedExperiment",
        "ReducedExperiment-class"
      ]
    },
    {
      "page": "enrichment",
      "title": "Functional enrichment analyses for dimensionally-reduced data",
      "topics": [
        "runEnrich",
        "runEnrich,FactorisedExperiment-method",
        "runEnrich,ModularExperiment-method"
      ]
    },
    {
      "page": "runICA",
      "title": "Run standard or stabilised Independent Component Analysis",
      "topics": [
        "runICA"
      ]
    },
    {
      "page": "runWGCNA",
      "title": "Run WGCNA for a data matrix",
      "topics": [
        "runWGCNA"
      ]
    },
    {
      "page": "sample_names",
      "title": "Get sample names",
      "topics": [
        "colnames<-,ReducedExperiment-method",
        "sampleNames",
        "sampleNames,ReducedExperiment-method",
        "sampleNames<-",
        "sampleNames<-,ReducedExperiment-method"
      ]
    },
    {
      "page": "show",
      "title": "Prints a summary of a ReducedExperiment object",
      "topics": [
        "show",
        "show,ReducedExperiment-method"
      ]
    },
    {
      "page": "stability",
      "title": "Get and setting the stability values for factors",
      "topics": [
        "stability",
        "stability,FactorisedExperiment-method",
        "stability<-",
        "stability<-,FactorisedExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/ReducedExperiment/raw/HEAD/README.md",
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