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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Microarray, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, ShinyApps, Software, Visualization |
| Version | 0.99.51 |
| 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 |
| Linking To | |
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| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GExPipe_0.99.51.tar.gz |
| Windows Binary (x86_64) | GExPipe_0.99.44.zip |
| macOS Binary (big-sur-x86_64) | GExPipe_0.99.51.tgz |
| macOS Binary (sonoma-arm64) | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/GExPipe/ |
| Package Short Url | https://bioconductor.org/packages/GExPipe/ |
| Package Downloads Report | Download Stats |