Package: GExPipe
Title: GExPipe: Gene Expression Pipeline Shiny Application
Version: 0.99.117
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).
        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.
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), 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, Biostrings, 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
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: 2026-10-27 22:25:41 UTC
RemoteUrl: https://github.com/bioc/GExPipe
RemoteRef: HEAD
RemoteSha: ddd5cafbf45b46916577d9a5154d103c4b57c411
NeedsCompilation: no
Packaged: 2026-10-28 00:10:30 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>