GExPipe: Gene Expression Pipeline Shiny Application

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Documentation for package ‘GExPipe’ version 0.99.43

• 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