Package: GExPipe
Title: GExPipe: Gene Expression Pipeline Shiny Application
Version: 0.99.43
Authors@R: c(
    person(
        given = "Safa",
        family = "Rafique",
        email = "safa.sandhu@gmail.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0003-2646-8106")
    ),
    person(
        given = "Naeem Mahmood",
        family = "Ashraf",
        email = "naeem.sbb@pu.edu.pk",
        role = "aut"
    ),
    person(
        given = "Prof. Dr. Muhammad Farooq",
        family = "Sabar",
        email = "farooq.sbb@pu.edu.pk",
        role = "aut"
    )
    )
Description: 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.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.5.0)
biocViews: Software, ShinyApps, GeneExpression, RNASeq, Microarray,
        DifferentialExpression, Normalization, Pathways, Network,
        NetworkEnrichment, Visualization
URL: https://github.com/safarafique/GExPipe
BugReports: https://github.com/safarafique/GExPipe/issues
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)
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
VignetteBuilder: knitr
Config/testthat/edition: 3
SystemRequirements: GNU make
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-22 09:28:43 UTC
RemoteUrl: https://github.com/bioc/GExPipe
RemoteRef: HEAD
RemoteSha: ffd15467eec4f74451eaf9d66a90b39897a765d8
NeedsCompilation: no
Packaged: 2026-07-22 16:17:51 UTC; root
Author: Safa Rafique [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2646-8106>),
  Naeem Mahmood Ashraf [aut],
  Prof. Dr. Muhammad Farooq Sabar [aut]
Maintainer: Safa Rafique <safa.sandhu@gmail.com>