Package: GeneTonic
Title: Enjoy Analyzing And Integrating The Results From Differential
        Expression Analysis And Functional Enrichment Analysis
Version: 3.4.0
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"
        )
    )
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 libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:56:40 UTC
RemoteUrl: https://github.com/bioc/GeneTonic
RemoteRef: RELEASE_3_22
RemoteSha: 21785a12d4ffe30af533d0db15b270d80d42be29
NeedsCompilation: no
Packaged: 2026-02-08 10:07:31 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]
Maintainer: Federico Marini <marinif@uni-mainz.de>
Built: R 4.5.2; ; 2026-02-08 10:11:15 UTC; windows
