Package: GExPipe
Title: GExPipe: Gene Expression Pipeline Shiny Application
Version: 0.99.114
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 (>= 4.6.0)
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, 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
git_url: https://git.bioconductor.org/packages/GExPipe
git_branch: devel
git_last_commit: b4905bf
git_last_commit_date: 2026-10-11
Repository: Bioconductor 3.24
Date/Publication: 2026-10-11
NeedsCompilation: no
Packaged: 2026-10-11 21:57:48 UTC; biocbuild
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>
