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  "Title": "Containers and tools for dimensionally-reduced -omics\nrepresentations",
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  "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).",
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        "[,ModularExperiment,ANY,ANY,ANY-method",
        "[,ReducedExperiment,ANY,ANY,ANY-method",
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        "[<-,ModularExperiment,ANY,ANY,ModularExperiment-method",
        "[<-,ReducedExperiment,ANY,ANY,ReducedExperiment-method"
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      "title": "Get and set module feature assignments",
      "topics": [
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        "assignments,ModularExperiment-method",
        "assignments<-",
        "assignments<-,ModularExperiment-method"
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      "title": "Calculate eigengenes for new data",
      "topics": [
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        "calcEigengenes,ModularExperiment,data.frame-method",
        "calcEigengenes,ModularExperiment,matrix-method",
        "calcEigengenes,ModularExperiment,SummarizedExperiment-method",
        "predict,ModularExperiment-method"
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      "title": "Combine ReducedExperiment objects by columns or rows",
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        "cbind,ModularExperiment-method",
        "cbind,ReducedExperiment-method",
        "cbind_rbind",
        "rbind,FactorisedExperiment-method",
        "rbind,ModularExperiment-method",
        "rbind,ReducedExperiment-method"
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      "title": "Get names of dimensionally-reduced components",
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        "componentNames,ReducedExperiment-method",
        "componentNames<-",
        "componentNames<-,FactorisedExperiment-method",
        "componentNames<-,ModularExperiment-method",
        "componentNames<-,ReducedExperiment-method",
        "moduleNames",
        "moduleNames,ModularExperiment-method",
        "moduleNames<-",
        "moduleNames<-,ModularExperiment-method"
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      "title": "Get the dendrogram stored in a ModularExperiment",
      "topics": [
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        "dendrogram,ModularExperiment-method",
        "dendrogram<-",
        "dendrogram<-,ModularExperiment-method"
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      "title": "Get the dimensions of a Reducedexperiment object",
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      "title": "Perform dimensionality reduction using Independent Component Analysis",
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    {
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      "title": "Estimate stability of factors as a function of the number of components",
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      "title": "FactorisedExperiment: A container for the results of factor analysis",
      "topics": [
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        "FactorisedExperiment",
        "FactorisedExperiment-class"
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        "getAlignedFeatures,FactorisedExperiment-method"
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      "title": "Get correlation of features with module eigengenes",
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        "getCentrality,ModularExperiment-method"
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      "topics": [
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    {
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      "title": "Gets alternative gene annotations from biomaRt",
      "topics": [
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        "getGeneIDs,ReducedExperiment-method"
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    },
    {
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      "topics": [
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    },
    {
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      "title": "Apply dimensionality reduction using Weighted Gene Correlation Network Analysis",
      "topics": [
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    },
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      "page": "loadings",
      "title": "Get and set loadings",
      "topics": [
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        "loadings,FactorisedExperiment-method",
        "loadings,ModularExperiment-method",
        "loadings<-",
        "loadings<-,FactorisedExperiment-method",
        "loadings<-,ModularExperiment-method"
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    },
    {
      "page": "modular_experiment",
      "title": "ModularExperiment: A container for the results of module analysis",
      "topics": [
        ".ModularExperiment",
        "ModularExperiment",
        "ModularExperiment-class"
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    },
    {
      "page": "modulePreservation",
      "title": "Get module preservation statistics",
      "topics": [
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    },
    {
      "page": "feature_names",
      "title": "Get feature names",
      "topics": [
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        "featureNames,ReducedExperiment-method",
        "featureNames<-",
        "featureNames<-,FactorisedExperiment-method",
        "featureNames<-,ModularExperiment-method",
        "featureNames<-,ReducedExperiment-method",
        "names<-,FactorisedExperiment-method",
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        "ROWNAMES<-,ReducedExperiment-method",
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      "page": "plotDendro",
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      "title": "ReducedExperiment",
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        "Relationship to existing Bioconductor packages",
        "Introducing ReducedExperiment containers with a case study",
        "The case study data",
        "Applying factor analysis",
        "Module analysis",
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