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  "Package": "LIPIDIFy",
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  "Title": "Comprehensive Lipidomics Data Analysis with Interactive\nVisualization",
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  "Description": "Provides a comprehensive toolkit for end-to-end lipidomics\ndata analysis, including missing value imputation, batch effect\ncorrection, normalization, differential abundance analysis\nusing limma and edgeR, gene set enrichment analysis, and\nextensive visualization capabilities. Lipid names are\nautomatically classified by class, subclass, and fatty-acid\nsaturation. Features both an interactive Shiny interface for\nbench biologists and fully scriptable R functions for\nbioinformaticians. Supports flexible custom lipid\nclassification schemes and user-defined enrichment sets.",
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  "Date/Publication": "2026-05-04 04:57:33 UTC",
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    "normalization",
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  "_exports": [
    "apply_normalizations",
    "classify_lipids",
    "correct_batch_effects",
    "create_default_contrasts",
    "create_enrichment_barplot",
    "create_enrichment_dotplot",
    "create_heatmap_robust",
    "create_lipid_expression_barplot",
    "create_pca_plot_with_ellipses",
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    "create_volcano_plot_labeled",
    "determine_saturation",
    "example_lipidomics_data",
    "export_classification",
    "fix_sample_alignment",
    "generate_example_data",
    "get_imputation_descriptions",
    "get_imputation_methods",
    "get_lipid_classification",
    "get_normalization_descriptions",
    "get_normalization_methods",
    "impute_missing_values",
    "launch_lipidomics_app",
    "load_custom_classification",
    "load_custom_enrichment_sets",
    "load_lipidomics_data",
    "load_lipidomics_data_from_df",
    "normalize_lipidomics_data",
    "normalize_log2median",
    "normalize_mean",
    "normalize_median",
    "normalize_pqn",
    "normalize_quantile",
    "normalize_tic",
    "normalize_vsn",
    "perform_differential_analysis",
    "perform_enrichment_analysis",
    "perform_pca",
    "perform_plsda",
    "test_saturation_classification",
    "visualize_raw_data",
    "visualize_raw_data_improved"
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    {
      "page": "apply_normalizations",
      "title": "Apply a Sequence of Normalization Methods",
      "topics": [
        "apply_normalizations"
      ]
    },
    {
      "page": "build_report_rmd_with_plots",
      "title": "Build the Rmd Content for the Analysis Report",
      "topics": [
        "build_report_rmd_with_plots"
      ]
    },
    {
      "page": "classify_lipids",
      "title": "Classify Lipids Based on Their Names",
      "topics": [
        "classify_lipids"
      ]
    },
    {
      "page": "convert_list_columns_to_strings",
      "title": "Convert List Columns to Strings",
      "topics": [
        "convert_list_columns_to_strings"
      ]
    },
    {
      "page": "correct_batch_effects",
      "title": "Correct Batch Effects from a Normalised Lipidomics Matrix",
      "topics": [
        "correct_batch_effects"
      ]
    },
    {
      "page": "create_default_contrasts",
      "title": "Create Default Contrasts",
      "topics": [
        "create_default_contrasts"
      ]
    },
    {
      "page": "create_enrichment_barplot",
      "title": "Create an Enrichment Barplot",
      "topics": [
        "create_enrichment_barplot"
      ]
    },
    {
      "page": "create_enrichment_dotplot",
      "title": "Create an Enrichment Dotplot",
      "topics": [
        "create_enrichment_dotplot"
      ]
    },
    {
      "page": "create_heatmap_robust",
      "title": "Create a Robust Heatmap of Top Variable Features",
      "topics": [
        "create_heatmap_robust"
      ]
    },
    {
      "page": "create_lipid_expression_barplot",
      "title": "Create a Lipid Expression Barplot Ordered by Group",
      "topics": [
        "create_lipid_expression_barplot"
      ]
    },
    {
      "page": "create_pathway_sets",
      "title": "Create Pathway Sets",
      "topics": [
        "create_pathway_sets"
      ]
    },
    {
      "page": "create_pca_plot_with_ellipses",
      "title": "Create a PCA Plot with Optional Confidence or Visual Ellipses",
      "topics": [
        "create_pca_plot_with_ellipses"
      ]
    },
    {
      "page": "create_pipeline_plot",
      "title": "Quick QC Plot for a Normalized Data Matrix",
      "topics": [
        "create_pipeline_plot"
      ]
    },
    {
      "page": "create_plsda_plot_with_ellipses",
      "title": "Create a PLS-DA Plot with Optional Ellipses",
      "topics": [
        "create_plsda_plot_with_ellipses"
      ]
    },
    {
      "page": "create_volcano_plot_labeled",
      "title": "Create a Volcano Plot with Optional Classification Colouring",
      "topics": [
        "create_volcano_plot_labeled"
      ]
    },
    {
      "page": "determine_saturation",
      "title": "Determine Fatty-Acid Saturation from a Lipid Name",
      "topics": [
        "determine_saturation"
      ]
    },
    {
      "page": "example_lipidomics_data",
      "title": "Example lipidomics dataset (lazy generator)",
      "topics": [
        "example_lipidomics_data"
      ]
    },
    {
      "page": "export_classification",
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      "topics": [
        "export_classification"
      ]
    },
    {
      "page": "fix_sample_alignment",
      "title": "Align Samples Between Data Matrix and Metadata",
      "topics": [
        "fix_sample_alignment"
      ]
    },
    {
      "page": "generate_example_data",
      "title": "Generate Example Dataset",
      "topics": [
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      ]
    },
    {
      "page": "get_imputation_descriptions",
      "title": "Return Human-Readable Descriptions of Imputation Methods",
      "topics": [
        "get_imputation_descriptions"
      ]
    },
    {
      "page": "get_imputation_methods",
      "title": "Return Available Imputation Method Names",
      "topics": [
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    },
    {
      "page": "get_lipid_classification",
      "title": "Get Lipid Classification",
      "topics": [
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      ]
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      "page": "get_normalization_descriptions",
      "title": "Return Human-Readable Descriptions of Normalization Methods",
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    },
    {
      "page": "get_normalization_methods",
      "title": "Return Available Normalization Method Names",
      "topics": [
        "get_normalization_methods"
      ]
    },
    {
      "page": "impute_missing_values",
      "title": "Impute Missing Values in a Lipidomics Data Matrix",
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        "impute_missing_values"
      ]
    },
    {
      "page": "launch_lipidomics_app",
      "title": "Launch the LIPIDIFy Shiny Application",
      "topics": [
        "launch_lipidomics_app"
      ]
    },
    {
      "page": "load_custom_classification",
      "title": "Load Custom Lipid Classification from a CSV File",
      "topics": [
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      ]
    },
    {
      "page": "load_custom_enrichment_sets",
      "title": "Load Custom Enrichment Sets from a CSV File",
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      ]
    },
    {
      "page": "load_lipidomics_data",
      "title": "Load Lipidomics Data",
      "topics": [
        "load_lipidomics_data"
      ]
    },
    {
      "page": "load_lipidomics_data_from_df",
      "title": "Load Lipidomics Data from Data Frame",
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      "page": "normalize_lipidomics_data",
      "title": "Normalize Lipidomics Data",
      "topics": [
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      "title": "Log2 Median Centering Normalization",
      "topics": [
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        "normalize_vsn"
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      "page": "normalize_mean",
      "title": "Mean Normalization",
      "topics": [
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      "title": "Quantile Normalization",
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        "normalize_quantile"
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      "page": "normalize_tic",
      "title": "TIC Normalization",
      "topics": [
        "normalize_tic"
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    {
      "page": "perform_differential_analysis",
      "title": "Perform Differential Analysis",
      "topics": [
        "perform_differential_analysis"
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      "title": "Perform Differential Analysis with EdgeR",
      "topics": [
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      "title": "Perform Enrichment Analysis",
      "topics": [
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      "title": "Run FGSEA with Error Handling",
      "topics": [
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    },
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      "page": "visualize_raw_data_improved",
      "title": "Visualize Raw or Normalized Data with Sample/Lipid Toggle",
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