# GExPipe: Gene Expression Pipeline Shiny Application

## Documentation for package ‘GExPipe’ version 0.99.51

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

## Help Pages

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_deseq2_design | DESeq2 design formula for count-based DE
gexpipe_de_sample_info | Summarise samples used in a DE run (transparency for mixed-platform runs)
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
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_normalize_and_intersect | Normalize microarray and RNA-seq datasets and compute common genes
gexp_no_common_genes_diagnostic_log | Build diagnostic log text when no common genes are found
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
runGExPipe | Run the GExPipe Shiny application