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    "tmodLimmaTest",
    "tmodLimmaTopTable",
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    "tmodPLAGEtest",
    "tmodSummary",
    "tmodTagcloud",
    "tmodUtest",
    "tmodZtest",
    "upset"
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      "class": [
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        "list"
      ],
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      "table": false,
      "tojson": true
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      "object": "Egambia",
      "file": "Egambia.rda",
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        "TB"
      ],
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      "table": true,
      "tojson": true
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      "object": "EgambiaResults",
      "file": "EgambiaResults.rda",
      "class": [
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      ],
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        "GENE_NAME",
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        "logFC",
        "AveExpr",
        "t",
        "P.Value",
        "adj.P.Val",
        "B"
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      "tojson": true
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      "object": "modmetabo",
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      "table": false,
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      "name": "tbmprof",
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      "table": true,
      "tojson": true
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    {
      "name": "tmod",
      "title": "Default gene expression module data",
      "object": "tmod",
      "file": "tmod.rda",
      "class": [
        "tmodGS",
        "list"
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      "fields": [],
      "table": false,
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    },
    {
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      "title": "Transcriptomic responses to vaccination",
      "object": "vaccination",
      "file": "vaccination.rda",
      "class": [
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        "logFC.F.D0",
        "qval.F.D0",
        "logFC.F.D1",
        "qval.F.D1",
        "logFC.F.D2",
        "qval.F.D2",
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      "title": "Transcriptional Module Analysis",
      "topics": [
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      ]
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      "topics": [
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      "topics": [
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      ]
    },
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      "topics": [
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        "EgambiaResults"
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    {
      "page": "eigengene",
      "title": "Calculate the eigengene of a module from a data set",
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    {
      "page": "evidencePlot",
      "title": "Create an evidence plot for a module",
      "topics": [
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    {
      "page": "filterGS",
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      "topics": [
        "filterGS",
        "showModule"
      ]
    },
    {
      "page": "getGenes",
      "title": "Get genes belonging to a gene set",
      "topics": [
        "getGenes"
      ]
    },
    {
      "page": "getModuleMembers",
      "title": "Return the contents of a gene set",
      "topics": [
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    {
      "page": "ggEvidencePlot",
      "title": "Create an evidence plot for a module (ggplot2 version)",
      "topics": [
        "ggEvidencePlot"
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    },
    {
      "page": "ggPanelplot",
      "title": "Create a tmod panel plot using ggplot",
      "topics": [
        "ggPanelplot"
      ]
    },
    {
      "page": "hgEnrichmentPlot",
      "title": "Create a visualisation of enrichment",
      "topics": [
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      ]
    },
    {
      "page": "makeTmodFromDataFrame",
      "title": "Convert a data frame to a tmod object",
      "topics": [
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      ]
    },
    {
      "page": "tmodGS-class",
      "title": "S3 class for tmod gene set collections",
      "topics": [
        "as_tmodGS",
        "length.tmodGS",
        "makeTmod",
        "makeTmodGS",
        "print.tmodGS",
        "[.tmod",
        "[.tmodGS"
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    {
      "page": "modCorPlot",
      "title": "Plot a correlation heatmap for modules",
      "topics": [
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    {
      "page": "modcors",
      "title": "Module correlation",
      "topics": [
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    },
    {
      "page": "modGroups",
      "title": "Find group of modules",
      "topics": [
        "modGroups"
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    },
    {
      "page": "modjaccard",
      "title": "Jaccard index for modules",
      "topics": [
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      ]
    },
    {
      "page": "modmetabo",
      "title": "Modules for metabolic profiling",
      "topics": [
        "modmetabo",
        "tbmprof"
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    {
      "page": "modOverlaps",
      "title": "Calculate overlaps of the modules",
      "topics": [
        "modOverlaps"
      ]
    },
    {
      "page": "pcaplot",
      "title": "Plot a PCA object returned by prcomp",
      "topics": [
        "pcaplot"
      ]
    },
    {
      "page": "pvalEffectPlot",
      "title": "Create an effect size / p-value plot",
      "topics": [
        "pvalEffectPlot"
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    },
    {
      "page": "showGene",
      "title": "A combined beeswarm / boxplot",
      "topics": [
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    {
      "page": "simplePie",
      "title": "Simple Pie Chart",
      "topics": [
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        "simplePie",
        "simpleRug"
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    },
    {
      "page": "tmod_ids",
      "title": "Query and set IDs of gene sets in a tmodGS object",
      "topics": [
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        "tmod_ids<-",
        "tmod_titles",
        "tmod_titles<-"
      ]
    },
    {
      "page": "tmod-data",
      "title": "Default gene expression module data",
      "topics": [
        "tmod",
        "tmod-data"
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    {
      "page": "tmod2DataFrame",
      "title": "Convert a tmod module set into a data frame",
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    {
      "page": "tmod2tmodGS",
      "title": "Convert the old tmod objects to the tmodGS objects",
      "topics": [
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    {
      "page": "tmodAUC",
      "title": "Calculate AUC",
      "topics": [
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    },
    {
      "page": "tmodDecideTests",
      "title": "Count the Up- or Down-regulated genes per module",
      "topics": [
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    {
      "page": "tmodImportMSigDB",
      "title": "Import data from MSigDB",
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      "page": "tmodLEA",
      "title": "Leading Edge Analysis",
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      "title": "Summary stats of a leading edge analysis",
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      "topics": [
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    {
      "page": "tmodPCA",
      "title": "PCA plot annotated with tmod",
      "topics": [
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      "page": "tmodSummary",
      "title": "Create a summary of multiple tmod analyses",
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    {
      "page": "tmodTagcloud",
      "title": "Tag cloud based on tmod results",
      "topics": [
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    {
      "page": "tmodUtest",
      "title": "Perform a statistical test of module expression",
      "topics": [
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        "tmodGeneSetTest",
        "tmodHGtest",
        "tmodPLAGEtest",
        "tmodUtest",
        "tmodZtest"
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    },
    {
      "page": "upset",
      "title": "Upset plot",
      "topics": [
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    },
    {
      "page": "vaccination",
      "title": "Transcriptomic responses to vaccination",
      "topics": [
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