Gene Set Enrichment Analysis Interactive Explorer

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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