Package: ExpHunterSuite
Title: Package for the Comprehensive Analysis of Transcriptomic Data
Version: 1.20.0
Author: James Perkins
Maintainer: James Perkins <jimrperkins@gmail.com>
Authors@R: c(
    person("James", "Perkins", email = "jimrperkins@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4108-096X")),
    person("Pedro", "Seoane Zonjic", email = "seoanezonjic@uma.es", role = "aut", comment = c(ORCID = "0000-0002-3020-1415")),
    person("Fernando", "Moreno Jabato", email = "fmjabato@gmail.com", role = "aut", comment = c(ORCID = "0000-0001-7498-1962")),
    person("José", "Córdoba Caballero", email = "josecordoba1995@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-1821-5742")),
    person("Elena", "Rojano Rivera", email = "elenarojano@outlook.com", role = "aut", comment = c(ORCID = "0000-0002-2678-710X")),
    person("Rocio", "Bautista Moreno", email = "rociobm@uma.es", role = "aut", comment = c(ORCID = "0000-0003-1685-8119")),
    person("M. Gonzalo", "Claros", email = "claros@uma.es", role = "aut", comment = c(ORCID = "0000-0002-0112-3550")),
    person("Isabel", "Gonzalez Gayte", email = "isabel.ggayte@gmail.com", role = "aut"),
    person("Juan Antonio", "García Ranea", email = "ranea@uma.es", role = "aut", comment = c(ORCID = "0000-0003-0327-1837"))
 )
Description: The ExpHunterSuite implements a comprehensive protocol for
        the analysis of transcriptional data using established R
        packages and combines their results. It covers key steps
        including differential expression analysis, co-expression
        analysis, and functional enrichment for RNA-seq data. The
        package provides interactive R functions as well as
        command-line scripts that wrap these functions.
License: MIT + file LICENSE
Depends: R (>= 4.1.0)
Imports: AnnotationDbi, annotatr, Biobase, BiocParallel,
        clusterProfiler, data.table, DESeq2, diffcoexp, DOSE, dplyr,
        DT, edgeR, enrichit, enrichplot, FactoInvestigate, FactoMineR,
        fastcluster, GenomicFeatures, GenomicRanges, ggplot2, ggrepel,
        ggridges, GO.db, graphics, grDevices, heatmaply, knitr, limma,
        magrittr, Matrix, matrixStats, miRBaseVersions.db, MKinfer,
        NOISeq, plyr, ReactomePA, rlang, rmarkdown, ROCR, stats,
        stringr, SummarizedExperiment, tidyr, topGO, tximport, utils,
        txdbmaker, WGCNA
Suggests: BiocGenerics, biomaRt, EnhancedVolcano, ggupset, naivebayes,
        optparse, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics,
        reshape2, testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: GeneExpressionWorkflow
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev libgmp3-dev make libmagick++-dev
        gsfonts libbz2-dev libicu-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev pari-gp libx11-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:44:49 UTC
RemoteUrl: https://github.com/bioc/ExpHunterSuite
RemoteRef: RELEASE_3_23
RemoteSha: 1960a2c9f7f2ae5f261065c1eb3b4229e4e7649c
NeedsCompilation: no
Packaged: 2026-10-04 17:18:59 UTC; root