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  "Title": "Analysis of Sex Differences in Omics Data for Complex Diseases",
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  "Authors@R": "c(\nperson(\"Enrico\", \"Glaab\", email = \"enrico.glaab@uni.lu\", role = c(\"aut\", \"cre\")),\nperson(\"Sophie\", \"Le Bars\", email = \"sophie.lebars@uni.lu\", role = \"aut\"),\nperson(\"Mohamed\", \"Soudy\", email = \"mohamed.soudy@uni.lu\", role = \"aut\"),\nperson(\"Murodzhon\", \"Akhmedov\", role = c(\"cph\"))\n)",
  "Maintainer": "Enrico Glaab <enrico.glaab@uni.lu>",
  "Description": "Tools to analyze sex differences in omics data for complex\ndiseases. It includes functions for differential expression\nanalysis using the 'limma' method <doi:10.1093/nar/gkv007>,\ninteraction testing between sex and disease, pathway enrichment\nwith 'clusterProfiler' <doi:10.1089/omi.2011.0118>, and gene\nregulatory network (GRN) construction and analysis using\n'igraph'. The package enables a reproducible workflow from raw\ndata processing to biological interpretation.",
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  "Author": "Enrico Glaab [aut, cre], Sophie Le Bars [aut], Mohamed Soudy\n[aut], Murodzhon Akhmedov [cph]",
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  "Date/Publication": "2026-05-11 18:11:53 UTC",
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    "generate_violinplot_bulk",
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    "get_top_hubs",
    "PCSF",
    "plot_enrichment_dotplots",
    "plot_network",
    "plot_network_pipeline",
    "plot_volcano_deg",
    "ppi_pipeline",
    "sex_interaction_analysis_bulk",
    "sex_interaction_analysis_sc",
    "sex_interaction_pipeline_sc",
    "sex_stratified_analysis_bulk",
    "sex_stratified_analysis_sc",
    "sex_stratified_pipeline_sc",
    "validate_input_bulk",
    "validate_input_sc"
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      "page": "categorize_sex",
      "title": "Compute sex-specific differentially expressed genes (DEGs) per category",
      "topics": [
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      ]
    },
    {
      "page": "categorized_enrich",
      "title": "Perform Pathway Enrichment Analysis for Pre-Categorized DEGs",
      "topics": [
        "categorized_enrich"
      ]
    },
    {
      "page": "construct_ppi_pcsf",
      "title": "Construct Protein-protein interaction Network using Prize-Collecting Steiner Forest",
      "topics": [
        "construct_ppi_pcsf"
      ]
    },
    {
      "page": "convert_gene_ids",
      "title": "Convert gene identifiers in a DEG table",
      "topics": [
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      ]
    },
    {
      "page": "generate_cat_report",
      "title": "Generate a Comprehensive Analysis Report",
      "topics": [
        "generate_cat_report"
      ]
    },
    {
      "page": "generate_dotplot_sc",
      "title": "Generate dotplot of selected genes across groups",
      "topics": [
        "generate_dotplot_sc"
      ]
    },
    {
      "page": "generate_violinplot_bulk",
      "title": "Generate Violin Plots for Bulk Expression Data",
      "topics": [
        "generate_violinplot_bulk"
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    },
    {
      "page": "get_string_network",
      "title": "Download and Process STRING Protein-Protein Interaction Network",
      "topics": [
        "get_string_network"
      ]
    },
    {
      "page": "get_top_hubs",
      "title": "Get Top Hub Genes by Betweenness Centrality",
      "topics": [
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      ]
    },
    {
      "page": "PCSF",
      "title": "Prize-collecting Steiner Forest (PCSF)",
      "topics": [
        "PCSF"
      ]
    },
    {
      "page": "plot_enrichment_dotplots",
      "title": "Create enrichment dotplots from enrichResult objects",
      "topics": [
        "plot_enrichment_dotplots"
      ]
    },
    {
      "page": "plot_network",
      "title": "Plot a condition-specific protein–protein interaction network with DEG annotations",
      "topics": [
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      ]
    },
    {
      "page": "plot_network_pipeline",
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      "topics": [
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    {
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      "title": "Generate volcano plots for categorized DEGs",
      "topics": [
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    },
    {
      "page": "ppi_pipeline",
      "title": "Run PPI PCSf pipeline for single cell DEG categories",
      "topics": [
        "ppi_pipeline"
      ]
    },
    {
      "page": "sex_interaction_analysis_bulk",
      "title": "Perform Sex-Phenotype Interaction Analysis for Bulk Data",
      "topics": [
        "sex_interaction_analysis_bulk"
      ]
    },
    {
      "page": "sex_interaction_analysis_sc",
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      "topics": [
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      ]
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      "page": "sex_interaction_pipeline_sc",
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        "sex_interaction_pipeline_sc"
      ]
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    {
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    {
      "page": "sex_stratified_analysis_sc",
      "title": "Perform sex-stratified differential expression analysis for single-cell Seurat object",
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      ]
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      "page": "sex_stratified_pipeline_sc",
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    },
    {
      "page": "validate_input_bulk",
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      "topics": [
        "validate_input_bulk"
      ]
    },
    {
      "page": "validate_input_sc",
      "title": "Validate single-cell input data for sex-stratified analysis",
      "topics": [
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      "filename": "XYomics_bulk_example.html",
      "title": "Bulk RNA-Seq Example",
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      "headings": [
        "Bulk RNA-Seq Analysis with XYomics",
        "Introduction",
        "Data Simulation",
        "Differential Expression Analysis Strategies",
        "Method 1: Sex-Stratified Analysis",
        "Identification of Sex-Specific Genes (from Stratified Analysis)",
        "Method 2: Interaction Term Analysis",
        "Visualization of Expression Patterns",
        "Pathway Enrichment Analysis",
        "Protein-protein Interaction Network Analysis",
        "1. Fetching the STRING Network",
        "2. Constructing the PCSF Network",
        "3. Visualizing the Network",
        "Generating a Report",
        "Conclusion"
      ],
      "created": "2025-11-13 21:20:08",
      "modified": "2026-05-11 18:11:53",
      "commits": 3
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      "filename": "XYomics_sc_example.html",
      "title": "Single Cell RNA-Seq Example",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Single-Cell RNA-Seq Analysis with XYomics",
        "Introduction",
        "Data Simulation and Preprocessing",
        "Simulating Single-Cell Data",
        "Preprocessing and Clustering",
        "Annotating Cell Types and Conditions",
        "Differential Expression Analysis Strategies",
        "Method 1: Sex-Stratified Analysis",
        "Method 2: Sex-Phenotype Interaction Analysis",
        "Visualization of Gene Expression",
        "Pathway Enrichment Analysis",
        "Protein-protein interaction Network Analysis",
        "Building the Network",
        "Visualizing the Network",
        "Generating a Report",
        "Notes"
      ],
      "created": "2025-11-13 21:20:08",
      "modified": "2026-05-11 18:11:53",
      "commits": 4
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