DESCRIPTION

Package: GeneTonic
Title: Enjoy Analyzing And Integrating The Results From Differential Expression 
    Analysis And Functional Enrichment Analysis
Version: 2.99.1
Date: 2024-10-06
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 = "Ludt", role = c("aut"), 
            email = "anneludt@uni-mainz.de", comment = c(ORCID = "0000-0002-2475-4945")
        )
    )
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: 7.3.2
Roxygen: list(markdown = TRUE)
biocViews:
    GUI, GeneExpression, Software, Transcription, Transcriptomics, Visualization,
    DifferentialExpression, Pathways, ReportWriting, GeneSetEnrichment, 
    Annotation, GO, ShinyApps