PCSF                    Prize-collecting Steiner Forest (PCSF)
categorize_sex          Compute sex-specific differentially expressed
                        genes (DEGs) per category
categorized_enrich      Perform Pathway Enrichment Analysis for
                        Pre-Categorized DEGs
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
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
