gexp_align_rnaseq_sample_names
                        Align RNA-seq count-matrix column names with
                        GEO sample metadata
gexp_batch_correct      Variance-based gene filtering and batch
                        correction
gexp_download_finalize_common_genes
                        Finalize common genes and combined matrix after
                        download/mapping
gexp_download_normalize_ids_for_overlap
                        Normalize dataset row IDs to gene symbols for
                        overlap
gexp_download_one_microarray_gse
                        Download and parse one microarray GSE
gexp_download_one_rnaseq_gse
                        Download and parse one RNA-seq GSE
gexp_fetch_geo_series_matrix_metadata
                        Fetch sample metadata from GEO series matrix
                        fallback
gexp_no_common_genes_diagnostic_log
                        Build diagnostic log text when no common genes
                        are found
gexp_normalize_and_intersect
                        Normalize microarray and RNA-seq datasets and
                        compute common genes
gexp_parse_gse_inputs   Parse GSE IDs from Shiny text inputs
gexp_prepare_download_dirs
                        Prepare clean download directories for current
                        run
gexp_qc_build_sample_dataset_map
                        Map combined-expression sample IDs to source
                        GSE datasets
gexp_qc_detect_outliers
                        Detect sample outliers from expression matrix
gexp_qc_exclude_samples
                        Exclude selected samples from download/QC state
                        lists
gexp_qc_gene_overlap_summary
                        Build gene-overlap summary table for QC UI
gexp_qc_prepare_boxplot_data
                        Prepare QC boxplot data from combined
                        expression
gexp_qc_prepare_density_data
                        Prepare density curves for QC density plot
gexp_qc_prepare_upset_data
                        Prepare UpSet matrix data from per-dataset
                        genes
gexp_qc_prepare_venn_sets
                        Prepare cleaned gene sets for Venn plotting
gexp_rebuild_all_genes_list
                        Rebuild per-dataset gene lists from
                        expression/count lists
gexp_run_de             Run differential expression analysis
gexp_wgcna_prepare      Prepare expression and sample data for WGCNA
gexpipe_analysis_report_text
                        Build reproducibility report text for export
gexpipe_batch_confounding_summary
                        Summarise Dataset x Condition confounding for
                        batch/DE guidance
gexpipe_batch_covariate_info
                        Summarise how Platform should enter batch/DE
                        models
gexpipe_build_batch_mod
                        Build ComBat / removeBatchEffect model matrix
                        (biology to preserve)
gexpipe_build_de_design
                        Build a model matrix for DE (limma / edgeR /
                        voom)
gexpipe_de_sample_info
                        Summarise samples used in a DE run
                        (transparency for mixed-platform runs)
gexpipe_deseq2_design   DESeq2 design formula for count-based DE
gexpipe_has_mixed_platforms
                        Detect microarray + RNA-seq in the same
                        analysis
gexpipe_independent_filter
                        Independent filtering for DE (limma
                        filterByExpr)
gexpipe_pca_polar_df    Polar PCA coordinates for batch/platform
                        diagnostic plots
gexpipe_platform_dataset_confounded
                        Test whether Platform is not estimable
                        alongside Dataset
gexpipe_pvca_df         Simplified PVCA variance bar-chart data (PCA +
                        per-factor R^2 on top PCs)
gexpipe_setup           Set up GExPipe dependencies and optionally
                        launch the app
gexpipe_wgcna_heatmap_cor
                        Drop redundant combined trait column from WGCNA
                        module-trait correlation matrix
runGExPipe              Run the GExPipe Shiny application
