Analysis of Sex Differences in Omics Data for Complex Diseases

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Documentation for package ‘XYomics’ version 0.1.1

• 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