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  "Package": "LIPIDIFy",
  "Type": "Package",
  "Title": "Comprehensive Lipidomics Data Analysis with Interactive\nVisualization",
  "Version": "0.99.7",
  "Authors@R": "c(\nperson(\"Fayrouz\", \"Hammal\", email = \"fayrouz.hammal@petermac.org\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7612-4953\")),\nperson(\"Karen\", \"Sheppard\", role = \"fnd\",\ncomment = \"NHMRC of Australia grant #2020050\")\n)",
  "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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  "Encoding": "UTF-8",
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  "biocViews": "Software, Lipidomics, MassSpectrometry, Normalization,\nPreprocessing, DifferentialExpression, GeneSetEnrichment,\nVisualization, ShinyApps, MultipleComparison, BatchEffect,\nQualityControl, DataImport, Classification",
  "URL": "https://github.com/fayrouzhammal/LIPIDIFy",
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  "Date/Publication": "2026-09-23 11:16:50 UTC",
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  "Author": "Fayrouz Hammal [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-7612-4953>),\nKaren Sheppard [fnd] (NHMRC of Australia grant #2020050)",
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    "message": "Address Bioconductor review: full data table, Tumour ID as factor, move data-prep script; bump to 0.99.7\n\n- Data Summary in the Shiny app shows the complete data table instead of head()\n- Tumour ID is stored as a factor; PCA and PLS-DA plots always use a\n  discrete colour scale for the grouping variable\n- Move prepare_ST001359_lipidomics.R from data-raw/ to inst/scripts/ and\n  remove data-raw/\n\nCo-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>\n",
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    "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",
    "create_pipeline_plot",
    "create_plsda_plot_with_ellipses",
    "create_volcano_plot_labeled",
    "determine_saturation",
    "export_classification",
    "fix_sample_alignment",
    "generate_example_data",
    "get_imputation_descriptions",
    "get_imputation_methods",
    "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_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": "classify_lipids",
      "title": "Classify Lipids Based on Their Names",
      "topics": [
        "classify_lipids"
      ]
    },
    {
      "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_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": "export_classification",
      "title": "Export Lipid Classification to CSV",
      "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": [
        "generate_example_data"
      ]
    },
    {
      "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": [
        "get_imputation_methods"
      ]
    },
    {
      "page": "get_normalization_descriptions",
      "title": "Return Human-Readable Descriptions of Normalization Methods",
      "topics": [
        "get_normalization_descriptions"
      ]
    },
    {
      "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",
      "topics": [
        "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",
      "topics": [
        "load_custom_enrichment_sets"
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    {
      "page": "load_lipidomics_data",
      "title": "Load Lipidomics Data",
      "topics": [
        "load_lipidomics_data"
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    {
      "page": "load_lipidomics_data_from_df",
      "title": "Load Lipidomics Data from Data Frame",
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      "page": "normalize_log2median",
      "title": "Log2 Median Centering Normalization",
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      "title": "Mean Normalization",
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      "title": "Quantile Normalization",
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      "title": "Perform Differential Analysis",
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      "title": "Perform Enrichment Analysis",
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    },
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      "title": "Test Saturation Classification",
      "topics": [
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    },
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      "title": "Visualize Raw Data",
      "topics": [
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    },
    {
      "page": "visualize_raw_data_improved",
      "title": "Visualize Raw or Normalized Data with Sample/Lipid Toggle",
      "topics": [
        "visualize_raw_data_improved"
      ]
    }
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        "Why LIPIDIFy?",
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        "Installation",
        "Example Data",
        "Lipid Classification",
        "Raw Data Visualization",
        "Normalization",
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        "Lipid Expression",
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        "Funding",
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      "modified": "2026-09-23 11:16:50",
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