Package: GeneTonic
Title: Enjoy Analyzing And Integrating The Results From Differential
        Expression Analysis And Functional Enrichment Analysis
Version: 3.7.0
Date: 2025-09-23
Authors@R: 
    c(
        person(
            given = "Federico", family = "Marini", role = c("aut", "cre"), 
            email = "marinif@uni-mainz.de", comment = c(ORCID = "0000-0003-3252-7758")
        ),
		    person(
            given = "Annekathrin", family = "Nedwed", role = c("aut"), 
            email = "anneludt@uni-mainz.de", comment = c(ORCID = "0000-0002-2475-4945")
        ),
        person(
            given = "Edoardo", family = "Filippi", role = c("ctb"), 
            email = "edoardo.filippi@uni-mainz.de", comment = c(ORCID = "0009-0003-9858-0137")
        )
    )
Description: This package provides functionality to combine the
        existing pieces of the transcriptome data and results, making
        it easier to generate insightful observations and hypothesis.
        Its usage is made easy with a Shiny application, combining the
        benefits of interactivity and reproducibility e.g. by capturing
        the features and gene sets of interest highlighted during the
        live session, and creating an HTML report as an artifact where
        text, code, and output coexist. Using the GeneTonicList as a
        standardized container for all the required components, it is
        possible to simplify the generation of multiple visualizations
        and summaries.
Depends: R (>= 4.0.0)
Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize,
        colorspace, colourpicker, ComplexHeatmap, ComplexUpset,
        dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce,
        ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics,
        grDevices, grid, igraph, matrixStats, methods, mosdef (>=
        1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown,
        S4Vectors, scales, shiny, shinyAce, shinycssloaders,
        shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools,
        utils, viridis, visNetwork
Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage,
        org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/federicomarini/GeneTonic
BugReports: https://github.com/federicomarini/GeneTonic/issues
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
biocViews: GUI, GeneExpression, Software, Transcription,
        Transcriptomics, Visualization, DifferentialExpression,
        Pathways, ReportWriting, GeneSetEnrichment, Annotation, GO,
        ShinyApps
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:51:46 UTC
RemoteUrl: https://github.com/bioc/GeneTonic
RemoteRef: HEAD
RemoteSha: d2ad76fbe2b5391212d16279b721aa4ed0cf26df
NeedsCompilation: no
Packaged: 2026-06-10 07:07:18 UTC; root
Author: Federico Marini [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3252-7758>),
  Annekathrin Nedwed [aut] (ORCID:
    <https://orcid.org/0000-0002-2475-4945>),
  Edoardo Filippi [ctb] (ORCID: <https://orcid.org/0009-0003-9858-0137>)
Maintainer: Federico Marini <marinif@uni-mainz.de>