Package: GExPipe 0.99.117

Safa Rafique

GExPipe: GExPipe: Gene Expression Pipeline Shiny Application

Shiny application (GExPipe) for high-throughput genomic analysis of bulk RNA-seq and microarray data (e.g. from GEO). Four analysis types: RNA-seq only, microarray only, Merged (Both) (per-dataset normalize then one joint batch and limma DE), and Parallel DE then merge (separate pipelines through DE, then RNA-seq intersect microarray). Each RNA-seq and microarray box accepts one or more GSE IDs in the same run. Integrates with Bioconductor (GEOquery, Biobase, limma, DESeq2, edgeR, clusterProfiler) for download, QC, normalization, batch correction, differential expression, WGCNA, pathway enrichment, PPI, and machine learning. Uses common data structures (ExpressionSet, DGEList) for interoperability. For a full dependency tree (including STRINGdb + PPI helpers), use BiocManager::install("GExPipe", dependencies = TRUE). STRING data are downloaded on first PPI use (internet required); they cannot be bundled in the package. Microarray CEL normalization uses affy and/or oligo when supplementary CEL files are available.

Authors:Safa Rafique [aut, cre], Naeem Mahmood Ashraf [aut], Prof. Dr. Muhammad Farooq Sabar [aut]

GExPipe_0.99.117.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GExPipe/json (API)

# Install 'GExPipe' in R:

install.packages('GExPipe', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/safarafique/gexpipe/issues

On BioConductor:GExPipe-0.99.116(bioc 3.24)

software shinyapps geneexpression rnaseq microarray differentialexpression normalization pathways network networkenrichment visualization

5.04 score 11 scripts 696 downloads 41 exports 306 dependencies

Last updated from:ddd5cafbf4. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	449
linux-devel	NOTE	608
source / vignettes	OK	719
linux-release	NOTE	675
macos-release	NOTE	411
macos-oldrel	NOTE	701
windows-devel	NOTE	536
windows-release	NOTE	671
windows-oldrel	NOTE	645
wasm-release	OK	460

Exports:gexp_align_rnaseq_sample_names gexp_batch_correct gexp_download_finalize_common_genes gexp_download_normalize_ids_for_overlap gexp_download_one_microarray_gse gexp_download_one_rnaseq_gse gexp_fetch_geo_series_matrix_metadata gexp_no_common_genes_diagnostic_log gexp_normalize_and_intersect gexp_parse_gse_inputs gexp_prepare_download_dirs gexp_qc_build_sample_dataset_map gexp_qc_detect_outliers gexp_qc_detect_outliers_per_dataset gexp_qc_exclude_samples gexp_qc_gene_overlap_summary gexp_qc_prepare_boxplot_data gexp_qc_prepare_density_data gexp_qc_prepare_upset_data gexp_qc_prepare_venn_sets gexp_rebuild_all_genes_list gexp_run_de gexp_wgcna_prepare gexpipe_analysis_report_text gexpipe_batch_confounding_summary gexpipe_batch_covariate_info gexpipe_build_batch_mod gexpipe_build_de_design gexpipe_consensus_degs gexpipe_de_sample_info gexpipe_deseq2_design gexpipe_has_mixed_platforms gexpipe_independent_filter gexpipe_pca_polar_df gexpipe_platform_dataset_confounded gexpipe_platform_sample_ids gexpipe_pvca_df gexpipe_run_limma_on_subset gexpipe_setup gexpipe_wgcna_heatmap_cor runGExPipe

Dependencies:abind affxparser affy affyio aisdk annotate AnnotationDbi ape aplot askpass assertthat babelgene backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel biomaRt Biostrings bit bit64 bitops blob boot broom bslib cachem callr car carData caret caTools checkmate chron circlize class cli clipr clock cluster clusterProfiler codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray Deriv DESeq2 diagram digest doBy doParallel DOSE dplyr DT dynamicTreeCut e1071 edgeR enrichit enrichplot evaluate farver fastcluster fastmap ff filelock fontawesome fontBitstreamVera fontLiberation fontquiver forcats foreach forecast foreign formatR Formula formula.tools fracdiff fs futile.logger futile.options future future.apply gdtools genefilter generics GenomicRanges GEOquery ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggsci ggsignif ggtangle ggtree glmnet GlobalOptions globals glue GO.db GOSemSim gower gplots graphlayouts gridExtra gridGraphics gson gsubfn gtable gtools hardhat hash haven highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 igraph impute ipred IRanges isoband iterators jomo jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later lattice lava lazyeval lifecycle limma listenv lme4 lmtest locfit logistf lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mice mime minqa mitml ModelMetrics modelr msigdbr multcomp mvtnorm nlme nloptr nnet numDeriv oligo oligoClasses openssl operator.tools ordinal org.Hs.eg.db otel pan parallelly patchwork pbkrtest pheatmap pillar pkgconfig plotrix plyr png polspline polyclip polynom preprocessCore prettyunits pROC processx prodlim progress progressr promises proto proxy ps purrr quantreg qvalue R.methodsS3 R.oo R.utils R6 randomForest rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr recipes reformulas rentrez reshape2 rlang rmarkdown rms rpart RSQLite rstatix rstudioapi S4Arrays S4Vectors S7 sandwich sass scales scatterpie Seqinfo shape shiny shinydashboard shinyjs snow sourcetools SparseArray SparseM sparsevctrs sqldf SQUAREM statmod STRINGdb stringi stringr SummarizedExperiment survival sva sys systemfonts TH.data tibble tidydr tidygraph tidyr tidyselect tidytree timechange timeDate tinytex treeio tweenr tzdb ucminf UpSetR urca utf8 vctrs VennDiagram viridis viridisLite vroom WGCNA withr xfun xgboost XML xml2 xtable XVector yaml yulab.utils zoo

GExPipe: An Integrated Pipeline for Gene Expression Analysis

Rendered fromGExPipe.Rmdusingknitr::rmarkdown

Last update: 2026-10-11
Started: 2026-03-29

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

Package: GExPipe 0.99.117

GExPipe: GExPipe: Gene Expression Pipeline Shiny Application

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