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: Development (3.24)
Shiny application (GExPipe) for high-throughput genomic analysis of bulk RNA-seq and microarray data (e.g. from GEO). Integrates with Bioconductor (GEOquery, Biobase, limma, DESeq2, edgeR, clusterProfiler) for a single workflow: 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("GExPipe")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("GExPipe")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("GExPipe")| Introduction to GExPipe | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, Microarray, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, ShinyApps, Software, Visualization |
| Version | 0.99.43 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | affy(>= 1.84.0), AnnotationDbi(>= 1.64.0), Biobase(>= 2.62.0), 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), 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), 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) |
| System Requirements | GNU make |
| URL | https://github.com/safarafique/GExPipe |
| Bug Reports | https://github.com/safarafique/GExPipe/issues |
See More
| 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), shinytest2, stringi, testthat |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GExPipe_0.99.43.tar.gz |
| Windows Binary (x86_64) | GExPipe_0.99.42.zip |
| macOS Binary (big-sur-x86_64) | GExPipe_0.99.42.tgz |
| macOS Binary (sonoma-arm64) | GExPipe_0.99.43.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GExPipe |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GExPipe |
| Bioc Package Browser | https://code.bioconductor.org/browse/GExPipe/ |
| Package Short Url | https://bioconductor.org/packages/GExPipe/ |
| Package Downloads Report | Download Stats |