batch_calc_gsea         Batch Parallel GSEA Calculation
build_edge_list_safely
                        Build Pathway Similarity Network Edges (Safe
                        Version)
build_gsea_pathways     Build GSEA Pathway Database with Interactive
                        Selection
build_hubgene_network   Build HubGene Network Data Structure (Enhanced
                        with Leading Edge)
calculate_overlap_ratio
                        Calculate ORA Ratio (for DotPlot)
color_by_direction      Color Nodes by Direction
creat_addition_data_rdsfile
                        Create Additional Data RDS File
create_addition_template
                        Create Additional Data Template
create_gsea_env         Define GseaEnv Class
create_gsea_res         Define GseaRes Class
create_gsea_task        Define GseaTask Class
extract_gsea_task       Extract GSEA Results for Specific Contrast
extract_hub_genes       Extract Hub Genes from Selected Pathways
                        (Enhanced with Leading Edge)
generate_boxplot_data_code
                        Generate Boxplot Expression-Data Extraction
                        Code
generate_boxplot_image_code
                        Generate Publication Boxplot Image Code
generate_combined_plot_code
                        Generate Combined Pathway Plotting Code
generate_de_volcano_code
                        Generate Publication DE Volcano Code
generate_dotplot_code   Generate Publication DotPlot Code
generate_gsea_html_report
                        Generate GSEA HTML Report
generate_hubgene_code   Generate Publication HubGene Network Code
generate_hubgene_hover_text
                        Generate HubGene Hover Text
generate_joint_canvas_code
                        Generate Joint Canvas Code
generate_network_code   Generate Publication Pathway Network Code
generate_pathway_plot_code
                        Generate Pathway Plotting Code
generate_volcano_code   Generate Publication Volcano Code
get_contrast_registry   Get Contrast Registry
get_core_genes_for_pathway
                        Extract Pathway Core Genes (Leading Edge)
get_core_genes_list     Batch Extract Core Genes for Multiple Pathways
get_de_table            Get Differential Expression Table
get_expr_matrix         Get Expression Matrix
get_geneset_info        Get Gene Set Information
get_hubgene_legend      Get Color Legend Configuration
get_sample_meta         Get Sample Metadata
get_term_genes          Get Full Pathway Gene Set (TERM2GENE)
gsea_pathwaysets_toy    Toy MSigDB pathway collection (Hallmark +
                        KEGG_LEGACY)
gsea_pathwaysets_toy_hallmark
                        Toy MSigDB pathway collection (Hallmark only)
GSEAlens-package        GSEAlens: Gene Set Enrichment Analysis
                        Interactive Explorer
import_gsea_capsule     Load and Smart-Relocate GSEA Computation
                        Capsule
inspect_gsea_env        View GSEA Environment Object Overview
inspect_gsea_res        View GSEA Result Overview
launch_gsea_app         GSEAlens Interactive Analysis Workstation
mod_ai_abs_page_server
                        AI Interpretation Page Server
plot_directional_gsea   Plot Directional GSEA
plot_gsea_memory        Plot GSEA Benchmark Memory Curve
precomputed_gseares     Pre-computed GSEA results from the airway
                        dataset
prepare_hubgene_nodes   Prepare HubGene Nodes for Plotting
preprocessed_dds        Pre-computed DESeq2 DESeqDataSet from the
                        airway dataset
preprocessed_dds_se     Pre-computed DESeqDataSet (SummarizedExperiment
                        form)
preprocessed_limma      Pre-computed limma-voom fit and DGEList from
                        the airway dataset
read_addition_data      Read Additional Data
setup_gsea_env          Initialize GSEA Environment Object
validate_param          Safe Parameter Validation with Fallback (Global
                        Strategy)
visualization           GSEA Visualization and Report Generation
