Analysis of Sex Differences in Omics Data for Complex Diseases

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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