# Gene Set Enrichment Analysis Interactive Explorer

## Documentation for package ‘GSEAlens’ version 0.99.35

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

GSEAlens-package | GSEAlens: Gene Set Enrichment Analysis Interactive Explorer
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
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
creat_addition_data_rdsfile | Create Additional Data RDS File
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)
GSEAlens | GSEAlens: Gene Set Enrichment Analysis Interactive Explorer
gsea_pathwaysets_toy | Toy MSigDB pathway collection (Hallmark + KEGG_LEGACY)
gsea_pathwaysets_toy_hallmark | Toy MSigDB pathway collection (Hallmark only)
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