GExPipe
This is the development version of GExPipe; to use it, please install the devel version of Bioconductor.
GExPipe: Gene Expression Pipeline Shiny Application
Bioconductor version: 3.24 · Package version: 0.99.51
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.
Author: Safa Rafique [aut, cre] 
, Naeem Mahmood Ashraf [aut], Prof. Dr. Muhammad Farooq Sabar [aut]
Maintainer: Safa Rafique <safa.sandhu at gmail.com>
Citation
From within R, enter citation("GExPipe"):
Safa Rafique, Naeem Mahmood Ashraf, Prof. Dr. Muhammad Farooq Sabar. GExPipe: GExPipe: Gene Expression Pipeline Shiny Application. doi:10.18129/B9.bioc.GExPipe, R package version 0.99.51, https://bioconductor.org/packages/GExPipe.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("GExPipe")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.51 |
| License | MIT + file LICENSE |
| URL | https://github.com/safarafique/GExPipe |
| Bug Reports | https://github.com/safarafique/GExPipe/issues |
| System Requirements | GNU make |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2376 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, Microarray, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, ShinyApps, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/GExPipe/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GExPipe")| GExPipe: An Integrated Pipeline for Gene Expression Analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | GExPipe_0.99.51.tar.gz |
| Windows binary (x86_64) | GExPipe_0.99.51.zip |
| macOS binary (arm64) | GExPipe_0.99.51.tgz |
| macOS binary (x86_64) | GExPipe_0.99.51.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GExPipe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GExPipe |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: affy (>= 1.84.0), AnnotationDbi (>= 1.64.0), Biobase (>= 2.62.0), BiocGenerics, biomaRt (>= 2.58.0), caret (>= 6.0.94), circlize (>= 0.4.16), cli (>= 3.6.0), clusterProfiler (>= 4.10.0), data.table (>= 1.15.0), DESeq2 (>= 1.42.0), dplyr (>= 1.1.0), DT (>= 0.30), dynamicTreeCut (>= 1.63.1), edgeR (>= 4.0.0), enrichplot (>= 1.22.0), GEOquery (>= 2.70.0), ggplot2 (>= 3.4.0), ggpubr (>= 0.6.0), ggraph (>= 2.2.0), ggrepel (>= 0.9.5), glmnet (>= 4.1.0), glue (>= 1.6.0), gridExtra (>= 2.3), igraph (>= 2.0.0), lifecycle (>= 1.0.0), limma (>= 3.58.0), logistf (>= 1.26.0), Matrix (>= 1.6.0), msigdbr (>= 7.5.1), oligo (>= 1.66.0), org.Hs.eg.db (>= 3.17.0), parallel, methods, pheatmap (>= 1.0.12), pillar (>= 1.9.0), pROC (>= 1.18.0), R.utils (>= 2.12.0), randomForest (>= 4.7.1), RColorBrewer (>= 1.1.3), Rcpp (>= 1.0.12), reshape2 (>= 1.4.4), rlang (>= 1.1.0), rms (>= 6.7.0), scales (>= 1.3.0), shiny (>= 1.8.0), shinydashboard (>= 0.7.2), shinyjs (>= 2.1.0), STRINGdb (>= 2.14.0), SummarizedExperiment (>= 1.32.0), sva (>= 3.50.0), tibble (>= 3.2.0), tidyr (>= 1.3.0), tidygraph (>= 1.3.0), UpSetR (>= 1.4.0), vctrs (>= 0.6.0), VennDiagram (>= 1.7.0), WGCNA (>= 1.72), withr (>= 2.5.0), xgboost (>= 1.7.0)
Suggests: BiocCheck, BiocManager, BiocStyle, Boruta (>= 8.0.0), bslib, car (>= 3.1.0), chromote, cicerone (>= 1.0.4), corrplot (>= 0.92), crosstalk, dcurves (>= 0.5.0), devtools, fontawesome, htmltools, htmlwidgets, kernlab (>= 0.9.32), knitr, mixOmics (>= 6.26.0), pak, pkgload, rmarkdown, remotes, SHAPforxgboost (>= 0.1.0), curl, httpuv, shinytest2, stringi, testthat