# Analysis of Sex Differences in Omics Data for Complex Diseases

## Documentation for package ‘XYomics’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

categorized_enrich_sc | Perform Pathway Enrichment Analysis for Pre-Categorized Differentially Expressed Genes (DEGs)
categorize_sex_sc | Compute sex-specific differentially expressed genes (DEGs) per category
construct_ppi_pcsf | Construct Protein-protein interaction Network using Prize-Collecting Steiner Forest
convertdf2enr | Convert Data Frame to enrichResult
generate_boxplot | Generate Boxplots for Expression Data
generate_cat_report | Generate a Comprehensive Analysis Report
generate_report | Generate a Comprehensive Analysis Report
get_string_network | Download and Process STRING Protein-Protein Interaction Network
identify_sex_specific_genes | Identify sex-specific and sex-dimorphic genes
improved_pathway_enrichment | Improved Pathway Enrichment Analysis
PCSF | Prize-collecting Steiner Forest (PCSF)
plot_network | Plot a Condition-Specific protein-protein interaction network with DEG Annotations
sex_interaction_analysis_bulk | Perform Sex-Phenotype Interaction Analysis for Bulk Data (Interaction Term)
sex_interaction_analysis_sc | Perform Sex-Phenotype Interaction Analysis for Single-Cell Data
sex_stratified_analysis_bulk | Perform differential expression analysis within each sex
sex_stratified_analysis_sc | Compute sex-specific differentially expressed genes (DEGs)
visualize_network | Visualize Gene Regulatory Network with Pie Charts