# Analysis of Sex Differences in Omics Data for Complex Diseases

## Documentation for package ‘XYomics’ version 0.1.4

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

## Help Pages

categorized_enrich | Perform Pathway Enrichment Analysis for Pre-Categorized DEGs
categorize_sex | Compute sex-specific differentially expressed genes (DEGs) per category
construct_ppi_pcsf | Construct Protein-protein interaction Network using Prize-Collecting Steiner Forest
convert_gene_ids | Convert gene identifiers in a DEG table
generate_cat_report | Generate a Comprehensive Analysis Report
generate_dotplot_sc | Generate dotplot of selected genes across groups
generate_violinplot_bulk | Generate Violin Plots for Bulk Expression Data
get_string_network | Download and Process STRING Protein-Protein Interaction Network
get_top_hubs | Get Top Hub Genes by Betweenness Centrality
PCSF | Prize-collecting Steiner Forest (PCSF)
plot_enrichment_dotplots | Create enrichment dotplots from enrichResult objects
plot_network | Plot a condition-specific protein–protein interaction network with DEG annotations
plot_network_pipeline | Generate protein-protein interaction network plots for single-cell DEGs
plot_volcano_deg | Generate volcano plots for categorized DEGs
ppi_pipeline | Run PPI PCSf pipeline for single cell DEG categories
sex_interaction_analysis_bulk | Perform Sex-Phenotype Interaction Analysis for Bulk Data
sex_interaction_analysis_sc | Perform Sex-Phenotype Interaction Analysis for Single-Cell Data
sex_interaction_pipeline_sc | Run sex phenotype interaction analysis pipeline for single cell data
sex_stratified_analysis_bulk | Perform differential expression analysis within each sex
sex_stratified_analysis_sc | Perform sex-stratified differential expression analysis for single-cell Seurat object
sex_stratified_pipeline_sc | Run sex stratified differential expression pipeline for single cell data
validate_input_bulk | Validate bulk input data for sex-stratified analysis
validate_input_sc | Validate single-cell input data for sex-stratified analysis