DESCRIPTION

Package: ideal
Type: Package
Title: Interactive Differential Expression AnaLysis
Version: 2.1.1
Date: 2024-12-19
Authors@R: c(person("Federico", "Marini", role = c("aut", "cre"), 
    email ="marinif@uni-mainz.de", 
    comment = c(ORCID = '0000-0003-3252-7758')))
Description: This package provides functions for an Interactive
    Differential Expression AnaLysis of RNA-sequencing datasets, to
    extract quickly and effectively information downstream the step
    of differential expression. A Shiny application encapsulates
    the whole package. Support for reproducibility of the whole analysis is 
    provided by means of a template report which gets automatically compiled 
    and can be stored/shared.
License: MIT + file LICENSE
Depends: topGO
Imports: 
    DESeq2, 
    SummarizedExperiment, 
    mosdef (>= 1.1.0),
    GenomicRanges, 
    IRanges,
    S4Vectors, 
    ggplot2 (>= 2.0.0), 
    heatmaply, 
    plotly,
    pheatmap,
    IHW, 
    gplots, 
    UpSetR, 
    goseq, 
    stringr, 
    dplyr,
    limma, 
    GOstats, 
    GO.db, 
    AnnotationDbi, 
    shiny (>= 0.12.0),
    shinydashboard, 
    shinyBS, 
    DT, 
    rentrez, 
    rintrojs, 
    rlang,
    ggrepel, 
    knitr,
    rmarkdown, 
    shinyAce, 
    BiocParallel, 
    grDevices, 
    graphics,
    base64enc,
    methods,
    utils,
    stats
Suggests: 
    testthat, 
    BiocStyle, 
    markdown,
    airway, 
    org.Hs.eg.db,
    TxDb.Hsapiens.UCSC.hg38.knownGene, 
    DEFormats, 
    htmltools,
    edgeR
URL: https://github.com/federicomarini/ideal,
    https://federicomarini.github.io/ideal/
BugReports: https://github.com/federicomarini/ideal/issues
biocViews: ImmunoOncology, GeneExpression, DifferentialExpression, RNASeq, Sequencing,
    Visualization, QualityControl, GUI, GeneSetEnrichment, ReportWriting, ShinyApps
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)