Package: ideal
Type: Package
Title: Interactive Differential Expression AnaLysis
Version: 2.5.0
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)
Config/pak/sysreqs: libcairo2-dev coinor-symphony
        coinor-libsymphony-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libmagick++-dev gsfonts libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-12-01 16:37:41 UTC
RemoteUrl: https://github.com/bioc/ideal
RemoteRef: HEAD
RemoteSha: 496947b407668b40a5aab8af0acaf7316f1bb0c6
NeedsCompilation: no
Packaged: 2026-01-31 08:24:30 UTC; root
Author: Federico Marini [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3252-7758>)
Maintainer: Federico Marini <marinif@uni-mainz.de>
Built: R 4.6.0; ; 2026-01-31 08:27:58 UTC; unix
