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    "plot_distribution_pTAI",
    "plot_distribution_pTAI_qqplot",
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    "plot_gene_space",
    "plot_mean_var",
    "plot_null_txi_sample",
    "plot_relative_expression_bar",
    "plot_relative_expression_line",
    "plot_sample_space",
    "plot_signature",
    "plot_signature_gene_quantiles",
    "plot_signature_multiple",
    "plot_signature_transformed",
    "plot_strata_expression",
    "PS_colours",
    "pTXI",
    "quantile_rank",
    "rel_exp_matrix",
    "relative_expression",
    "remove_genes",
    "rename_phyex_set",
    "save_gatai_results_pdf",
    "ScPhyloExpressionSet",
    "ScPhyloExpressionSet_from_matrix",
    "ScPhyloExpressionSet_from_seurat",
    "select_genes",
    "set_expression",
    "stat_early_conservation_test",
    "stat_flatline_test",
    "stat_late_conservation_test",
    "stat_pairwise_test",
    "stat_reductive_hourglass_test",
    "stat_reverse_hourglass_test",
    "strata_enrichment",
    "sTXI",
    "TAI",
    "taxid",
    "TDI",
    "TEI",
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    "TXI",
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      "title": "Example phyex set",
      "object": "example_phyex_set",
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        "myTAI::PhyloExpressionSetBase",
        "S7_object"
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      "table": false,
      "tojson": false
    },
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      "title": "Example phyex set old",
      "object": "example_phyex_set_old",
      "class": [
        "myTAI::BulkPhyloExpressionSet",
        "myTAI::PhyloExpressionSetBase",
        "S7_object"
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      "table": false,
      "tojson": false
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    {
      "name": "example_phyex_set_sc",
      "title": "Load Example Single-Cell PhyloExpressionSet",
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      "class": [
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        "myTAI::PhyloExpressionSetBase",
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      "title": "Age Category Specific apply Function",
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      "title": "as_BulkPhyloExpressionSet",
      "topics": [
        "as_BulkPhyloExpressionSet"
      ]
    },
    {
      "page": "as_data_frame",
      "title": "Convert BulkPhyloExpressionSet to Data Frame",
      "topics": [
        "as_data_frame"
      ]
    },
    {
      "page": "BulkPhyloExpressionSet",
      "title": "Bulk PhyloExpressionSet Class",
      "topics": [
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      "title": "Convert Data to BulkPhyloExpressionSet",
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      "title": "Check if object is a BulkPhyloExpressionSet",
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      "title": "Check if object is a PhyloExpressionSet",
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      "title": "Check if object is a ScPhyloExpressionSet",
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      "page": "collapse",
      "title": "Collapse PhyloExpressionSet Replicates",
      "topics": [
        "collapse"
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    {
      "page": "ConservationTestResult",
      "title": "Conservation Test Result S7 Class",
      "topics": [
        "ConservationTestResult"
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    },
    {
      "page": "COUNT_TRANSFORMS",
      "title": "Count Transformation Functions",
      "topics": [
        "COUNT_TRANSFORMS"
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    },
    {
      "page": "destroy_pattern",
      "title": "Destroy Phylotranscriptomic Pattern Using GATAI",
      "topics": [
        "destroy_pattern"
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    },
    {
      "page": "diagnose_test_robustness",
      "title": "Diagnose Test Robustness",
      "topics": [
        "diagnose_test_robustness"
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    {
      "page": "Distribution",
      "title": "Distribution S7 Class",
      "topics": [
        "Distribution"
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      "page": "distributions",
      "title": "Predefined Distribution Objects",
      "topics": [
        "distributions"
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    },
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      "page": "downsample",
      "title": "Downsample ScPhyloExpressionSet",
      "topics": [
        "downsample"
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    {
      "page": "downsample_expression",
      "title": "Downsample Expression Matrix by Groups",
      "topics": [
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    {
      "page": "example_phyex_set",
      "title": "Example phyex set",
      "topics": [
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      "page": "genes_lowly_expressed",
      "title": "Select Lowly Expressed Genes",
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      "title": "Gene Expression Filtering Functions",
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      "title": "Select Top Mean Expressed Genes",
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      "title": "Normalise Stage Expression Data",
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      "title": "Compute TXI Profiles Omitting Each Gene",
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      "title": "Permute Strata in PhyloExpressionSet",
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      "title": "PhyloExpressionSet Base Class",
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    {
      "page": "plot_contribution",
      "title": "Plot Phylostratum Contribution to Transcriptomic Index",
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    {
      "page": "plot_cullen_frey",
      "title": "Plot Cullen-Frey Diagram for Distribution Assessment",
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    {
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      "title": "Comparing expression levels distributions across developmental stages",
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    {
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      "title": "QQ plot comparing partial TAI distributions across developmental stages against a reference stage",
      "topics": [
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    },
    {
      "page": "plot_distribution_strata",
      "title": "Plot Distribution of Genes Across Phylostrata",
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    {
      "page": "plot_gatai_results",
      "title": "Plot Comprehensive GATAI Results",
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    {
      "page": "plot_gene_heatmap",
      "title": "Plot Gene Expression Heatmap",
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      "title": "Plot Individual Gene Expression Profiles",
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      "title": "Plot Gene Space Using PCA",
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      "title": "Plot Mean-Variance Relationship",
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      "title": "Plot Transcriptomic Signature",
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      "title": "Plot Multiple Transcriptomic Signatures",
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      "title": "Plot Expression Levels by Phylostratum",
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    {
      "page": "PS_colours",
      "title": "Generate Phylostratum Colors",
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      "title": "Calculate Quantile Ranks",
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      "title": "Rename a PhyloExpressionSet",
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      "title": "Late Conservation Test",
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      "title": "Pairwise Conservation Test",
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